EC 4.1.1.1     
Accepted name: pyruvate decarboxylase
Reaction: a 2-oxo carboxylate = an aldehyde + CO2
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): α-carboxylase (ambiguous); pyruvic decarboxylase; α-ketoacid carboxylase; 2-oxo-acid carboxy-lyase
Systematic name: 2-oxo-acid carboxy-lyase (aldehyde-forming)
Comments: A thiamine-diphosphate protein. Also catalyses acyloin formation.
References:
1.  Singer, T.P. and Pensky, J. Isolation and properties of the α-carboxylase of wheat germ. J. Biol. Chem. 196 (1952) 375–388. [PMID: 12980978]
[EC 4.1.1.1 created 1961]
 
 
EC 4.1.1.2     
Accepted name: oxalate decarboxylase
Reaction: oxalate + H+ = formate + CO2
Other name(s): oxalate carboxy-lyase
Systematic name: oxalate carboxy-lyase (formate-forming)
Comments: The enzyme from Bacillus subtilis contains manganese and requires O2 for activity, even though there is no net redox change.
References:
1.  Jakoby, W.B., Ohmura, E. and Hayaishi, O. Enzymatic decarboxylation of oxalic acid. J. Biol. Chem. 222 (1956) 435–446. [PMID: 13367015]
2.  Tanner, A. and Bornemann, S. Bacillus subtilis YvrK is an acid-induced oxalate decarboxylase. J. Bacteriol. 182 (2000) 5271–5273. [PMID: 10960116]
3.  Tanner, A., Bowater, L., Fairhurst, S.A. and Bornemann, S. Oxalate decarboxylase requires manganese and dioxygen for activity: Overexpression and characterization of Bacillus subtilis YvrK and YoaN. J. Biol. Chem. 276 (2001) 43627–43634. [PMID: 11546787]
[EC 4.1.1.2 created 1961]
 
 
EC 4.1.1.3      
Transferred entry: oxaloacetate decarboxylase. Now recognized to be two enzymes EC 7.2.4.2 [oxaloacetate decarboxylase (Na+ extruding)] and EC 4.1.1.112 (oxaloacetate decarboxylase).
[EC 4.1.1.3 created 1961 as EC 4.1.1.3, modified 1986, modified 2000, deleted 2018]
 
 
EC 4.1.1.4     
Accepted name: acetoacetate decarboxylase
Reaction: acetoacetate + H+ = acetone + CO2
Other name(s): acetoacetic acid decarboxylase; acetoacetate carboxy-lyase
Systematic name: acetoacetate carboxy-lyase (acetone-forming)
References:
1.  Davies, R. Studies of the acetone-butanol fermentation. 4. Acetoacetic acid decarboxylase of Cl. acetobutylicum (BY). Biochem. J. 37 (1943) 230–238. [PMID: 16747621]
2.  Zerner, B., Coutts, S.M., Lederer, F., Waters, H.H. and Westheimer, F.H. Acetoacetate decarboxylase. Preparation of the enzyme. Biochemistry 5 (1966) 813–816. [PMID: 5911291]
3.  Ho, M.C., Menetret, J.F., Tsuruta, H. and Allen, K.N. The origin of the electrostatic perturbation in acetoacetate decarboxylase. Nature 459 (2009) 393–397. [PMID: 19458715]
[EC 4.1.1.4 created 1961]
 
 
EC 4.1.1.5     
Accepted name: acetolactate decarboxylase
Reaction: (2S)-2-hydroxy-2-methyl-3-oxobutanoate = (3R)-3-hydroxybutan-2-one + CO2
Other name(s): α-acetolactate decarboxylase; (S)-2-hydroxy-2-methyl-3-oxobutanoate carboxy-lyase; (S)-2-hydroxy-2-methyl-3-oxobutanoate carboxy-lyase [(R)-2-acetoin-forming]; (S)-2-hydroxy-2-methyl-3-oxobutanoate carboxy-lyase [(3R)-3-hydroxybutan-2-one-forming]
Systematic name: (2S)-2-hydroxy-2-methyl-3-oxobutanoate carboxy-lyase [(3R)-3-hydroxybutan-2-one-forming]
References:
1.  Hill, R.K., Sawada, S. and Arfin, S.M. Stereochemistry of valine and isoleucine biosynthesis. IV. Synthesis, configuration, and enzymatic specificity of α-acetolactate and α-aceto-α-hydroxybutyrate. Bioorg. Chem. 8 (1979) 175–189.
2.  Størmer, F.C. Isolation of crystalline pH 6 acetolactate-forming enzyme from Aerobacter aerogenes. J. Biol. Chem. 242 (1967) 1756–1759. [PMID: 6024768]
[EC 4.1.1.5 created 1961]
 
 
EC 4.1.1.6     
Accepted name: cis-aconitate decarboxylase
Reaction: cis-aconitate = itaconate + CO2
Glossary: itaconate = 2-methylenesuccinate
cis-aconitate = (Z)-prop-1-ene-1,2,3-tricarboxylate
Other name(s): cis-aconitic decarboxylase; cis-aconitate carboxy-lyase; CAD1 (gene name); IRG1 (gene name)
Systematic name: cis-aconitate carboxy-lyase (itaconate-forming)
Comments: The enzyme has been characterized from the fungus Aspergillus terreus and from human macrophages. cf. EC 4.1.1.113, trans-aconitate decarboxylase.
References:
1.  Bentley, R. and Thiessen, C.P. Biosynthesis of itaconic acid in Aspergillus terreus. III. The properties and reaction mechanism of cis-aconitic acid decarboxylase. J. Biol. Chem. 226 (1957) 703–720. [PMID: 13438855]
2.  Dwiarti, L., Yamane, K., Yamatani, H., Kahar, P. and Okabe, M. Purification and characterization of cis-aconitic acid decarboxylase from Aspergillus terreus TN484-M1. J. Biosci. Bioeng. 94 (2002) 29–33. [PMID: 16233265]
3.  Kanamasa, S., Dwiarti, L., Okabe, M. and Park, E.Y. Cloning and functional characterization of the cis-aconitic acid decarboxylase (CAD) gene from Aspergillus terreus. Appl. Microbiol. Biotechnol. 80 (2008) 223–229. [PMID: 18584171]
4.  Michelucci, A., Cordes, T., Ghelfi, J., Pailot, A., Reiling, N., Goldmann, O., Binz, T., Wegner, A., Tallam, A., Rausell, A., Buttini, M., Linster, C.L., Medina, E., Balling, R. and Hiller, K. Immune-responsive gene 1 protein links metabolism to immunity by catalyzing itaconic acid production. Proc. Natl. Acad. Sci. USA 110 (2013) 7820–7825. [PMID: 23610393]
[EC 4.1.1.6 created 1961, modified 2018]
 
 
EC 4.1.1.7     
Accepted name: benzoylformate decarboxylase
Reaction: phenylglyoxylate = benzaldehyde + CO2
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
phenylglyoxylate = benzoylformate = 2-oxo-2-phenylacetate
Other name(s): phenylglyoxylate decarboxylase; benzoylformate carboxy-lyase; benzoylformate carboxy-lyase (benzaldehyde-forming)
Systematic name: phenylglyoxylate carboxy-lyase (benzaldehyde-forming)
Comments: A thiamine-diphosphate protein.
References:
1.  Gunsalus, C.F., Stanier, R.Y. and Gunsalus, I.C. The enzymatic conversion of mandelic acid to benzoic acid. III. Fractionation and properties of the soluble enzymes. J. Bacteriol. 66 (1953) 548–553. [PMID: 13108854]
[EC 4.1.1.7 created 1961]
 
 
EC 4.1.1.8     
Accepted name: oxalyl-CoA decarboxylase
Reaction: oxalyl-CoA = formyl-CoA + CO2
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): oxalyl coenzyme A decarboxylase; oxalyl-CoA carboxy-lyase
Systematic name: oxalyl-CoA carboxy-lyase (formyl-CoA-forming)
Comments: A thiamine-diphosphate protein.
References:
1.  Quayle, J.R. Carbon assimilation by Pseudomonas oxalaticus (OX1). 7. Decarboxylation of oxalyl-coenzyme A to formyl-coenzyme A. Biochem. J. 89 (1963) 492–503. [PMID: 14101969]
[EC 4.1.1.8 created 1961]
 
 
EC 4.1.1.9     
Accepted name: malonyl-CoA decarboxylase
Reaction: malonyl-CoA = acetyl-CoA + CO2
Other name(s): malonyl coenzyme A decarboxylase; malonyl-CoA carboxy-lyase
Systematic name: malonyl-CoA carboxy-lyase (acetyl-CoA-forming)
Comments: Specific for malonyl-CoA. The enzyme from Pseudomonas ovalis also catalyses the reaction of EC 2.8.3.3 malonate CoA-transferase.
References:
1.  Buckner, J.S., Kolattudy, P.E. and Poulose, A.J. Purification and properties of malonyl-coenzyme A decarboxylase, a regulatory enzyme from the uropygial gland of goose. Arch. Biochem. Biophys. 177 (1976) 539–551. [PMID: 827976]
2.  Takamura, Y. and Kitayama, Y. Purification and some properties of malonate decarboxylase from Pseudomonas ovalis: an oligomeric enzyme with bifunctional properties. Biochem. Int. 3 (1981) 483–491.
[EC 4.1.1.9 created 1961, deleted 1972, reinstated 1978]
 
 
EC 4.1.1.10      
Deleted entry: aminomalonate decarboxylase. Now included with EC 4.1.1.12, aspartate 4-decarboxylase
[EC 4.1.1.10 created 1961, deleted 1972]
 
 
EC 4.1.1.11     
Accepted name: aspartate 1-decarboxylase
Reaction: L-aspartate = β-alanine + CO2
Other name(s): aspartate α-decarboxylase; L-aspartate α-decarboxylase; aspartic α-decarboxylase; L-aspartate 1-carboxy-lyase
Systematic name: L-aspartate 1-carboxy-lyase (β-alanine-forming)
Comments: The Escherichia coli enzyme contains a pyruvoyl group.
References:
1.  Williamson, J.M. and Brown, G.M. Purification and properties of L-aspartate-α-decarboxylase, an enzyme that catalyzes the formation of β-alanine in Escherichia coli. J. Biol. Chem. 254 (1979) 8074–8082. [PMID: 381298]
[EC 4.1.1.11 created 1961, deleted 1972, reinstated 1984]
 
 
EC 4.1.1.12     
Accepted name: aspartate 4-decarboxylase
Reaction: L-aspartate = L-alanine + CO2
Other name(s): desulfinase; aminomalonic decarboxylase; aspartate β-decarboxylase; aspartate ω-decarboxylase; aspartic ω-decarboxylase; aspartic β-decarboxylase; L-aspartate β-decarboxylase; cysteine sulfinic desulfinase; L-cysteine sulfinate acid desulfinase; L-aspartate 4-carboxy-lyase
Systematic name: L-aspartate 4-carboxy-lyase (L-alanine-forming)
Comments: A pyridoxal-phosphate protein. Also catalyses the decarboxylation of aminomalonate (formerly listed as EC 4.1.1.10), and the desulfination of 3-sulfino-L-alanine to sulfite and alanine.
References:
1.  Kakimoto, T., Kato, J., Shibitani, T., Nishimura, N. and Chibata, I. Crystalline L-aspartate β-decarboxylase of Pseudomonas dacunhae. I. Crystallization and some physiocochemical properties. J. Biol. Chem. 244 (1969) 353–358. [PMID: 5773301]
2.  Novogrodsky, A. and Meister, A. Control of aspartate β-decarboxylase activity by transamination. J. Biol. Chem. 239 (1964) 879–888. [PMID: 14154469]
3.  Palekar, A.G., Tate, S.S. and Meister, A. Inhibition of aspartate β-decarboxylase by aminomalonate. Stereospecific decarboxylation of aminomalonate to glycine. Biochemistry 9 (1970) 2310–2315. [PMID: 5424207]
4.  Wilson, E.M. and Kornberg, H.L. Properties of crystalline L-aspartate 4-carboxy-lyase from Achromobacter sp. Biochem. J. 88 (1963) 578–587. [PMID: 14071532]
[EC 4.1.1.12 created 1961, modified 1976 (EC 4.1.1.10 created 1961, incorporated 1972)]
 
 
EC 4.1.1.13      
Deleted entry:  carbamoylaspartate decarboxylase
[EC 4.1.1.13 created 1961, deleted 1972]
 
 
EC 4.1.1.14     
Accepted name: valine decarboxylase
Reaction: L-valine = 2-methylpropanamine + CO2
Other name(s): leucine decarboxylase; L-valine carboxy-lyase
Systematic name: L-valine carboxy-lyase (2-methylpropanamine-forming)
Comments: A pyridoxal-phosphate protein. Also acts on L-leucine.
References:
1.  Sutton, C.R. and King, H.K. Inhibition of leucine decarboxylase by thiol-binding reagents. Arch. Biochem. Biophys. 96 (1962) 360–370. [PMID: 13918558]
[EC 4.1.1.14 created 1961]
 
 
EC 4.1.1.15     
Accepted name: glutamate decarboxylase
Reaction: L-glutamate = 4-aminobutanoate + CO2
Glossary: 4-aminobutanoate = γ-aminobutyrate = GABA
Other name(s): L-glutamic acid decarboxylase; L-glutamic decarboxylase; cysteic acid decarboxylase; L-glutamate α-decarboxylase; aspartate 1-decarboxylase; aspartic α-decarboxylase; L-aspartate-α-decarboxylase; γ-glutamate decarboxylase; L-glutamate 1-carboxy-lyase
Systematic name: L-glutamate 1-carboxy-lyase (4-aminobutanoate-forming)
Comments: A pyridoxal-phosphate protein. The brain enzyme also acts on L-cysteate, 3-sulfino-L-alanine and L-aspartate.
References:
1.  Ambe, L. and Sohonie, K. Purification and properties of glutamate decarboxylase from the field bean (Dolichos lablab). Enzymologia 26 (1963) 98–107. [PMID: 14081858]
2.  Nakano, Y. and Kitaoka, S. L-Aspartate α-decarboxylase in a cell-free system from Escherichia coli. J. Biochem. (Tokyo) 70 (1971) 327. [PMID: 4937550]
3.  Roberts, E. and Frankel, S. Further studies of glutamic acid decarboxylase in brain. J. Biol. Chem. 190 (1951) 505–512. [PMID: 14841200]
[EC 4.1.1.15 created 1961]
 
 
EC 4.1.1.16     
Accepted name: hydroxyglutamate decarboxylase
Reaction: 3-hydroxy-L-glutamate = 4-amino-3-hydroxybutanoate + CO2
Other name(s): 3-hydroxy-L-glutamate 1-carboxy-lyase
Systematic name: 3-hydroxy-L-glutamate 1-carboxy-lyase (4-amino-3-hydroxybutanoate-forming)
Comments: A pyridoxal-phosphate protein.
References:
1.  Umbreit, W.W. and Heneage, P. β-Hydroxyglutamic acid decarboxylase. J. Biol. Chem. 201 (1953) 15–20. [PMID: 13044771]
[EC 4.1.1.16 created 1961]
 
 
EC 4.1.1.17     
Accepted name: ornithine decarboxylase
Reaction: L-ornithine = putrescine + CO2
Glossary: putrescine = butane-1,4-diamine
Other name(s): SpeC; L-ornithine carboxy-lyase
Systematic name: L-ornithine carboxy-lyase (putrescine-forming)
Comments: A pyridoxal-phosphate protein.
References:
1.  Ono, M., Inoue, H., Suzuki, F. and Takeda, Y. Studies on ornithine decarboxylase from the liver of thioacetamide-treated rats. Purification and some properties. Biochim. Biophys. Acta 284 (1972) 285–297. [PMID: 5073764]
2.  Taylor, E.S. and Gale, E.F. Studies on bacterial amino-acid decarboxylases. 6. Codecarboxylase content and action of inhibitors. Biochem. J. 39 (1945) 52–58. [PMID: 16747854]
[EC 4.1.1.17 created 1961]
 
 
EC 4.1.1.18     
Accepted name: lysine decarboxylase
Reaction: L-lysine = cadaverine + CO2
Other name(s): L-lysine carboxy-lyase
Systematic name: L-lysine carboxy-lyase (cadaverine-forming)
Comments: A pyridoxal-phosphate protein. Also acts on 5-hydroxy-L-lysine.
References:
1.  Gale, E.F. and Epps, H.M.R. Studies on bacterial amino-acid decarboxylases. 1. l(+)-lysine decarboxylase. Biochem. J. 38 (1944) 232–242. [PMID: 16747785]
2.  Soda, K. and Moriguchi, M. Crystalline lysine decarboxylase. Biochem. Biophys. Res. Commun. 34 (1969) 34–39. [PMID: 5762458]
[EC 4.1.1.18 created 1961]
 
 
EC 4.1.1.19     
Accepted name: arginine decarboxylase
Reaction: L-arginine = agmatine + CO2
Glossary: agmatine = (4-aminobutyl)guanidine
Other name(s): SpeA; L-arginine carboxy-lyase
Systematic name: L-arginine carboxy-lyase (agmatine-forming)
Comments: A pyridoxal-phosphate protein.
References:
1.  Blethen, S.L., Boeker, E.A. and Snell, E.E. Arginine decarboxylase from Escherichia coli. I. Purification and specificity for substrates and coenzyme. J. Biol. Chem. 243 (1968) 1671–1677. [PMID: 4870599]
2.  Ramakrishna, S. and Adiga, P.R. Arginine decarboxylase from Lathyrus sativus seedlings. Purification and properties. Eur. J. Biochem. 59 (1975) 377–386. [PMID: 1252]
3.  Taylor, E.S. and Gale, E.F. Studies on bacterial amino-acid decarboxylases. 6. Codecarboxylase content and action of inhibitors. Biochem. J. 39 (1945) 52–58. [PMID: 16747854]
[EC 4.1.1.19 created 1961]
 
 
EC 4.1.1.20     
Accepted name: diaminopimelate decarboxylase
Reaction: meso-2,6-diaminoheptanedioate = L-lysine + CO2
Other name(s): diaminopimelic acid decarboxylase; meso-diaminopimelate decarboxylase; DAP-decarboxylase; meso-2,6-diaminoheptanedioate carboxy-lyase
Systematic name: meso-2,6-diaminoheptanedioate carboxy-lyase (L-lysine-forming)
Comments: A pyridoxal-phosphate protein.
References:
1.  Denman, R.F., Hoare, D.S. and Work, E. Diaminopimelic acid decarboxylase in pyridoxin-deficient Escherichia coli. Biochim. Biophys. Acta 16 (1955) 442–443. [PMID: 14378182]
[EC 4.1.1.20 created 1961]
 
 
EC 4.1.1.21     
Accepted name: phosphoribosylaminoimidazole carboxylase
Reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate = 5-amino-1-(5-phospho-D-ribosyl)imidazole + CO2
Other name(s): 5-phosphoribosyl-5-aminoimidazole carboxylase; 5-amino-1-ribosylimidazole 5-phosphate carboxylase; AIR carboxylase; 1-(5-phosphoribosyl)-5-amino-4-imidazolecarboxylate carboxy-lyase; ADE2; class II PurE; 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate carboxy-lyase
Systematic name: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate carboxy-lyase [5-amino-1-(5-phospho-D-ribosyl)imidazole-forming]
Comments: While this is the reaction that occurs in vertebrates during purine biosynthesis, two enzymes are required to carry out the same reaction in Escherichia coli, namely EC 6.3.4.18, 5-(carboxyamino)imidazole ribonucleotide synthase and EC 5.4.99.18, 5-(carboxyamino)imidazole ribonucleotide mutase [3]. 5-Carboxyamino-1-(5-phospho-D-ribosyl)imidazole is not a substrate.
References:
1.  Lukens, L.N. and Buchanan, J.M. Biosynthesis of purines. XXIV. The enzymatic synthesis of 5-amino-1-ribosyl-4-imidazolecarboxylic acid 5′-phosphate from 5-amino-1-ribosylimidazole 5′-phosphate and carbon dioxide. J. Biol. Chem. 234 (1959) 1799–1805. [PMID: 13672967]
2.  Firestine, S.M., Poon, S.W., Mueller, E.J., Stubbe, J. and Davisson, V.J. Reactions catalyzed by 5-aminoimidazole ribonucleotide carboxylases from Escherichia coli and Gallus gallus: a case for divergent catalytic mechanisms. Biochemistry 33 (1994) 11927–11934. [PMID: 7918411]
3.  Firestine, S.M., Misialek, S., Toffaletti, D.L., Klem, T.J., Perfect, J.R. and Davisson, V.J. Biochemical role of the Cryptococcus neoformans ADE2 protein in fungal de novo purine biosynthesis. Arch. Biochem. Biophys. 351 (1998) 123–134. [PMID: 9500840]
[EC 4.1.1.21 created 1961, modified 2000, modified 2006]
 
 
EC 4.1.1.22     
Accepted name: histidine decarboxylase
Reaction: L-histidine = histamine + CO2
Other name(s): L-histidine decarboxylase; L-histidine carboxy-lyase
Systematic name: L-histidine carboxy-lyase (histamine-forming)
Comments: A pyridoxal-phosphate protein (in animal tissues). The bacterial enzyme has a pyruvoyl residue as prosthetic group.
References:
1.  Epps, H.M.R. Studies on bacterial amino-acid decarboxylases. 4. l(–)-Histidine decarboxylase from Cl. welchii type A. Biochem. J. 39 (1945) 42–46. [PMID: 16747851]
2.  Riley, W.O. and Snell, E.E. Histidine decarboxylase of Lactobacillus 30a. IV. The presence of covalently bound pyruvate as the prosthetic group. Biochemistry 7 (1968) 3520–3528. [PMID: 5681461]
3.  Rosenthaler, J., Guirard, B.M., Chang, G.W. and Snell, E.E. Purification and properties of histidine decarboxylase from Lactobacillus 30a. Proc. Natl. Acad. Sci. USA 54 (1965) 152–158. [PMID: 5216347]
[EC 4.1.1.22 created 1961]
 
 
EC 4.1.1.23     
Accepted name: orotidine-5′-phosphate decarboxylase
Reaction: orotidine 5′-phosphate = UMP + CO2
Other name(s): orotidine-5′-monophosphate decarboxylase; orotodylate decarboxylase; orotidine phosphate decarboxylase; OMP decarboxylase; orotate monophosphate decarboxylase; orotidine monophosphate decarboxylase; orotidine phosphate decarboxylase; OMP-DC; orotate decarboxylase; orotidine 5′-phosphate decarboxylase; orotidylic decarboxylase; orotidylic acid decarboxylase; orotodylate decarboxylase; ODCase; orotic decarboxylase; orotidine-5′-phosphate carboxy-lyase
Systematic name: orotidine-5′-phosphate carboxy-lyase (UMP-forming)
Comments: The enzyme from higher eukaryotes is identical with EC 2.4.2.10 orotate phosphoribosyltransferase .
References:
1.  Jones, M.E., Kavipurapu, P.R. and Traut, T.W. Orotate phosphoribosyltransferase: orotidylate decarboxylase (Ehrlich ascites cell). Methods Enzymol. 51 (1978) 155–167. [PMID: 692383]
2.  Lieberman, I., Kornberg, A. and Simms, E.S. Enzymatic synthesis of pyrimidine nucleotides. Orotidine-5′-phosphate and uridine-5′-phosphate. J. Biol. Chem. 215 (1955) 403–415. [PMID: 14392174]
3.  McClard, R.W., Black, M.J., Livingstone, L.R. and Jones, M.E. Isolation and initial characterization of the single polypeptide that synthesizes uridine 5′-monophosphate from orotate in Ehrlich ascites carcinoma. Purification by tandem affinity chromatography of uridine-5′-monophosphate synthase. Biochemistry 19 (1980) 4699–4706. [PMID: 6893554]
[EC 4.1.1.23 created 1961, modified 1986]
 
 
EC 4.1.1.24     
Accepted name: aminobenzoate decarboxylase
Reaction: 4(or 2)-aminobenzoate = aniline + CO2
Systematic name: aminobenzoate carboxy-lyase (aniline-forming)
Comments: A pyridoxal-phosphate protein.
References:
1.  McCullough, W.G., Piligian, J.T. and Daniel, I.J. Enzymatic decarboxylation of three aminobenzoates. J. Am. Chem. Soc. 79 (1957) 628–630.
[EC 4.1.1.24 created 1961]
 
 
EC 4.1.1.25     
Accepted name: tyrosine decarboxylase
Reaction: L-tyrosine = tyramine + CO2
Other name(s): L-tyrosine decarboxylase; L-(-)-tyrosine apodecarboxylase; L-tyrosine carboxy-lyase
Systematic name: L-tyrosine carboxy-lyase (tyramine-forming)
Comments: A pyridoxal-phosphate protein. The bacterial enzyme also acts on 3-hydroxytyrosine and, more slowly, on 3-hydroxyphenylalanine.
References:
1.  McGilvery, R.W. and Cohen, P.P. The decarboxylation of L-phenylalanine by Streptococcus faecalis R. J. Biol. Chem. 174 (1948) 813–816. [PMID: 18871240]
[EC 4.1.1.25 created 1961]
 
 
EC 4.1.1.26      
Deleted entry:  DOPA decarboxylase. Now included with EC 4.1.1.28 aromatic-L-amino-acid decarboxylase
[EC 4.1.1.26 created 1961, deleted 1972]
 
 
EC 4.1.1.27      
Deleted entry:  tryptophan decarboxylase. Now included with EC 4.1.1.28 aromatic-L-amino-acid decarboxylase
[EC 4.1.1.27 created 1961, deleted 1972]
 
 
EC 4.1.1.28     
Accepted name: aromatic-L-amino-acid decarboxylase
Reaction: (1) L-dopa = dopamine + CO2
(2) 5-hydroxy-L-tryptophan = 5-hydroxytryptamine + CO2
Glossary: dopamine = 4-(2-aminoethyl)benzene-1,2-diol
L-dopa = 3,4-dihydroxyphenylalanine
Other name(s): DOPA decarboxylase; tryptophan decarboxylase; hydroxytryptophan decarboxylase; L-DOPA decarboxylase; aromatic amino acid decarboxylase; 5-hydroxytryptophan decarboxylase; aromatic-L-amino-acid carboxy-lyase (tryptamine-forming)
Systematic name: aromatic-L-amino-acid carboxy-lyase
Comments: A pyridoxal-phosphate protein. The enzyme also acts on some other aromatic L-amino acids, including L-tryptophan, L-tyrosine and L-phenylalanine.
References:
1.  Christenson, J.G., Dairman, W. and Udenfriend, S. On the identity of DOPA decarboxylase and 5-hydroxytryptophan decarboxylase (immunological titration-aromatic L-amino acid decarboxylase-serotonin-dopamine-norepinephrine). Proc. Natl. Acad. Sci. USA 69 (1972) 343–347. [PMID: 4536745]
2.  Lovenberg, W., Weissbach, H. and Udenfriend, S. Aromatic L-amino acid decarboxylase. J. Biol. Chem. 237 (1962) 89–93. [PMID: 14466899]
3.  McGilvery, R.W. and Cohen, P.P. The decarboxylation of L-phenylalanine by Streptococcus faecalis R. J. Biol. Chem. 174 (1948) 813–816. [PMID: 18871240]
4.  Sekeris, C.E. Zur Tyrosinstoffwechsel der Insekten. XII. Reinigung, Eigenschaften und Substratspezifität der DOPA-Decarboxylase. Hoppe-Seyler's Z. Physiol. Chem. 332 (1963) 70–78. [PMID: 14054806]
5.  Weissbach, H., Bogdanski, D.F., Redfield, B.G. and Udenfriend, S. Studies on the effect of vitamin B6 on 5-hydroxytryptamine (serotonin) formation. J. Biol. Chem. 227 (1957) 617–624. [PMID: 13462983]
[EC 4.1.1.28 created 1961 (EC 4.1.1.26 and EC 4.1.1.27 both created 1961 and incorporated 1972)]
 
 
EC 4.1.1.29     
Accepted name: sulfinoalanine decarboxylase
Reaction: 3-sulfino-L-alanine = hypotaurine + CO2
Other name(s): cysteine-sulfinate decarboxylase; L-cysteinesulfinic acid decarboxylase; cysteine-sulfinate decarboxylase; CADCase/CSADCase; CSAD; cysteic decarboxylase; cysteinesulfinic acid decarboxylase; cysteinesulfinate decarboxylase; sulfoalanine decarboxylase; 3-sulfino-L-alanine carboxy-lyase
Systematic name: 3-sulfino-L-alanine carboxy-lyase (hypotaurine-forming)
Comments: A pyridoxal-phosphate protein. Also acts on L-cysteate. The 1992 edition of the Enzyme List erroneously gave the name sulfoalanine decarboxylase to this enzyme.
References:
1.  Guion-Rain, M.C., Portemer, C. and Chatagner, F. Rat liver cysteine sulfinate decarboxylase: purification, new appraisal of the molecular weight and determination of catalytic properties. Biochim. Biophys. Acta 384 (1975) 265–276. [PMID: 236774]
2.  Jacobsen, J.G., Thomas, L.L. and Smith, L.H., Jr. Properties and distribution of mammalian L-cysteine sulfinate carboxy-lyases. Biochim. Biophys. Acta 85 (1964) 103–116. [PMID: 14159288]
[EC 4.1.1.29 created 1961, deleted 1972, reinstated 1976, modified 1983, modified 1999]
 
 
EC 4.1.1.30     
Accepted name: pantothenoylcysteine decarboxylase
Reaction: N-[(R)-pantothenoyl]-L-cysteine = pantetheine + CO2
Other name(s): pantothenylcysteine decarboxylase; N-[(R)-pantothenoyl]-L-cysteine carboxy-lyase
Systematic name: N-[(R)-pantothenoyl]-L-cysteine carboxy-lyase (pantetheine-forming)
References:
1.  Brown, G.M. Pantothenylcysteine, a precursor of pantotheine in Lactobacillus helveticus. J. Biol. Chem. 226 (1957) 651–661. [PMID: 13438850]
[EC 4.1.1.30 created 1961]
 
 
EC 4.1.1.31     
Accepted name: phosphoenolpyruvate carboxylase
Reaction: phosphate + oxaloacetate = phosphoenolpyruvate + HCO3-
Other name(s): phosphopyruvate (phosphate) carboxylase; PEP carboxylase; phosphoenolpyruvic carboxylase; PEPC; PEPCase; phosphate:oxaloacetate carboxy-lyase (phosphorylating)
Systematic name: phosphate:oxaloacetate carboxy-lyase (adding phosphate, phosphoenolpyruvate-forming)
Comments: This enzyme replenishes oxaloacetate in the tricarboxylic acid cycle when operating in the reverse direction. The reaction proceeds in two steps: formation of carboxyphosphate and the enolate form of pyruvate, followed by carboxylation of the enolate and release of phosphate.
References:
1.  Chen, J.H. and Jones, R.F. Multiple forms of phosphoenolpyruvate carboxylase from Chlamydomonas reeinhardtii. Biochim. Biophys. Acta 214 (1970) 318–325. [PMID: 5501374]
2.  Mazelis, M. and Vennesland, B. Carbon dioxide fixation into oxalacetate in higher plants. Plant Physiol. 32 (1957) 591–600. [PMID: 16655053]
3.  Tovar-Mendez, A., Mujica-Jimenez, C. and Munoz-Clares, R.A. Physiological implications of the kinetics of maize leaf phosphoenolpyruvate carboxylase. Plant Physiol. 123 (2000) 149–160. [PMID: 10806233]
[EC 4.1.1.31 created 1961, modified 2011]
 
 
EC 4.1.1.32     
Accepted name: phosphoenolpyruvate carboxykinase (GTP)
Reaction: GTP + oxaloacetate = GDP + phosphoenolpyruvate + CO2
Other name(s): phosphoenolpyruvate carboxylase (ambiguous); phosphopyruvate carboxylase (ambiguous); phosphopyruvate (guanosine triphosphate) carboxykinase; phosphoenolpyruvic carboxykinase (GTP); phosphopyruvate carboxylase (GTP); phosphoenolpyruvic carboxylase (GTP); phosphoenolpyruvic carboxykinase (ambiguous); phosphoenolpyruvate carboxykinase (ambiguous); PEP carboxylase (ambiguous); GTP:oxaloacetate carboxy-lyase (transphosphorylating)
Systematic name: GTP:oxaloacetate carboxy-lyase (adding GTP; phosphoenolpyruvate-forming)
Comments: ITP can act as phosphate donor.
References:
1.  Change, H.-C. and Lane, M.D. The enzymatic carboxylation of phosphoenolpyruvate. II. Purification and properties of liver mitochondrial phosphoenolpyruvate carboxykinase. J. Biol. Chem. 241 (1966) 2413–2420. [PMID: 5911620]
2.  Kurahashi, K., Pennington, R.J. and Utter, M.J. Nucleotide specificity of oxalacetic carboxylase. J. Biol. Chem. 226 (1957) 1059–1075. [PMID: 13438893]
[EC 4.1.1.32 created 1961]
 
 
EC 4.1.1.33     
Accepted name: diphosphomevalonate decarboxylase
Reaction: ATP + (R)-5-diphosphomevalonate = ADP + phosphate + isopentenyl diphosphate + CO2
Other name(s): pyrophosphomevalonate decarboxylase; mevalonate-5-pyrophosphate decarboxylase; pyrophosphomevalonic acid decarboxylase; 5-pyrophosphomevalonate decarboxylase; mevalonate 5-diphosphate decarboxylase; ATP:(R)-5-diphosphomevalonate carboxy-lyase (dehydrating)
Systematic name: ATP:(R)-5-diphosphomevalonate carboxy-lyase (adding ATP; isopentenyl-diphosphate-forming)
References:
1.  Bloch, K., Chaykin, S., Phillips, A.H. and de Waard, A. Mevalonic acid pyrophosphate and isopentenyl pyrophosphate. J. Biol. Chem. 234 (1959) 2595–2604. [PMID: 13801508]
[EC 4.1.1.33 created 1961]
 
 
EC 4.1.1.34     
Accepted name: dehydro-L-gulonate decarboxylase
Reaction: 3-dehydro-L-gulonate = L-xylulose + CO2
Other name(s): keto-L-gulonate decarboxylase; 3-keto-L-gulonate decarboxylase; 3-dehydro-L-gulonate carboxy-lyase
Systematic name: 3-dehydro-L-gulonate carboxy-lyase (L-xylulose-forming)
References:
1.  Smiley, J.D. and Ashwell, G. Purification and properties of β-L-hydroxy acid dehydrogenase. II. Isolation of β-keto-L-gluconic acid, an intermediate in L-xylulose biosynthesis. J. Biol. Chem. 236 (1961) 357–364.
[EC 4.1.1.34 created 1965]
 
 
EC 4.1.1.35     
Accepted name: UDP-glucuronate decarboxylase
Reaction: UDP-D-glucuronate = UDP-D-xylose + CO2
Other name(s): uridine-diphosphoglucuronate decarboxylase; UDP-D-glucuronate carboxy-lyase
Systematic name: UDP-D-glucuronate carboxy-lyase (UDP-D-xylose-forming)
Comments: Requires NAD+.
References:
1.  Ankel, H. and Feingold, D.S. Biosynthesis of uridine diphosphate D-xylose. 1. Uridine diphosphate glucuronate carboxy-lyase of wheat germ. Biochemistry 4 (1965) 2468–2475.
[EC 4.1.1.35 created 1965]
 
 
EC 4.1.1.36     
Accepted name: phosphopantothenoylcysteine decarboxylase
Reaction: N-[(R)-4′-phosphopantothenoyl]-L-cysteine = pantotheine 4′-phosphate + CO2
Other name(s): 4-phosphopantotheoylcysteine decarboxylase; 4-phosphopantothenoyl-L-cysteine decarboxylase; PPC-decarboxylase; N-[(R)-4′-phosphopantothenoyl]-L-cysteine carboxy-lyase
Systematic name: N-[(R)-4′-phosphopantothenoyl]-L-cysteine carboxy-lyase (pantotheine-4′-phosphate-forming)
References:
1.  Brown, G.M. Requirement of cytidine triphosphate for the biosynthesis of phosphopantetheine. J. Am. Chem. Soc. 80 (1958) 3161.
2.  Brown, G.M. The metabolism of pantothenic acid. J. Biol. Chem. 234 (1959) 370–378. [PMID: 13630913]
[EC 4.1.1.36 created 1965]
 
 
EC 4.1.1.37     
Accepted name: uroporphyrinogen decarboxylase
Reaction: uroporphyrinogen III = coproporphyrinogen III + 4 CO2
Other name(s): uroporphyrinogen III decarboxylase; porphyrinogen carboxy-lyase; porphyrinogen decarboxylase; uroporphyrinogen-III carboxy-lyase
Systematic name: uroporphyrinogen-III carboxy-lyase (coproporphyrinogen-III-forming)
Comments: Acts on a number of porphyrinogens.
References:
1.  Mauzerall, D. and Granick, S. Porphyrin biosynthesis in erythrocytes. III. Uroporphyrinogen and its decarboxylase. J. Biol. Chem. 232 (1958) 1141–1162. [PMID: 13549492]
2.  Tomio, J.M., Garcia, R.C., San Martin de Viale, L.C. and Grinstein, M. Porphyrin biosynthesis. VII. Porphyrinogen carboxy-lyase from avian erythrocytes. Purification and properties. Biochim. Biophys. Acta 198 (1970) 353–363. [PMID: 4984554]
[EC 4.1.1.37 created 1965]
 
 
EC 4.1.1.38     
Accepted name: phosphoenolpyruvate carboxykinase (diphosphate)
Reaction: diphosphate + oxaloacetate = phosphate + phosphoenolpyruvate + CO2
Other name(s): phosphopyruvate carboxylase (ambiguous); PEP carboxyphosphotransferase (ambiguous); PEP carboxykinase (ambiguous); phosphopyruvate carboxykinase (pyrophosphate); PEP carboxylase (ambiguous); phosphopyruvate carboxykinase (ambiguous); phosphoenolpyruvic carboxykinase (ambiguous); phosphoenolpyruvic carboxylase (ambiguous); phosphoenolpyruvate carboxytransphosphorylase (ambiguous); phosphoenolpyruvate carboxykinase (ambiguous); phosphoenolpyruvic carboxykinase; phosphoenolpyruvic carboxylase; PEPCTrP; phosphoenolpyruvic carboxykinase (pyrophosphate); phosphoenolpyruvic carboxylase (pyrophosphate); phosphoenolpyruvate carboxylase (ambiguous); phosphoenolpyruvate carboxyphosphotransferase (ambiguous); phosphoenolpyruvic carboxytransphosphorylase (ambiguous); phosphoenolpyruvate carboxylase (pyrophosphate); phosphopyruvate carboxylase (pyrophosphate); diphosphate:oxaloacetate carboxy-lyase (transphosphorylating)
Systematic name: diphosphate:oxaloacetate carboxy-lyase (transphosphorylating; phosphoenolpyruvate-forming)
Comments: Also catalyses the reaction: phosphoenolpyruvate + phosphate = pyruvate + diphosphate.
References:
1.  Lochmuller, H., Wood, H.G. and Davis, J.J. Phosphoenolpyruvate carboxytransphosphorylase. II. Crystallization and properties. J. Biol. Chem. 241 (1966) 5678–5691. [PMID: 4288896]
[EC 4.1.1.38 created 1965]
 
 
EC 4.1.1.39     
Accepted name: ribulose-bisphosphate carboxylase
Reaction: 2 3-phospho-D-glycerate + 2 H+ = D-ribulose 1,5-bisphosphate + CO2 + H2O
Other name(s): D-ribulose 1,5-diphosphate carboxylase; D-ribulose-1,5-bisphosphate carboxylase; RuBP carboxylase; carboxydismutase; diphosphoribulose carboxylase; ribulose 1,5-bisphosphate carboxylase; ribulose 1,5-bisphosphate carboxylase/oxygenase; ribulose 1,5-diphosphate carboxylase; ribulose 1,5-diphosphate carboxylase/oxygenase; ribulose bisphosphate carboxylase/oxygenase; ribulose diphosphate carboxylase; ribulose diphosphate carboxylase/oxygenase; rubisco; 3-phospho-D-glycerate carboxy-lyase (dimerizing)
Systematic name: 3-phospho-D-glycerate carboxy-lyase (dimerizing; D-ribulose-1,5-bisphosphate-forming)
Comments: Will utilize O2 instead of CO2, forming 3-phospho-D-glycerate and 2-phosphoglycolate.
References:
1.  Bowles, G., Ogren, W.L. and Hageman, R.H. Phosphoglycolate production catalyzed by ribulose diphosphate carboxylase. Biochem. Biophys. Res. Commun. 45 (1971) 716–722. [PMID: 4331471]
2.  Wishnick, M., Lane, M.D., Scrutton, M.C. and Mildvan, A.S. The presence of tightly bound copper in ribulose diphosphate carboxylase from spinach. J. Biol. Chem. 244 (1969) 5761–5763. [PMID: 4310607]
[EC 4.1.1.39 created 1965, modified 2001, modified 2003]
 
 
EC 4.1.1.40     
Accepted name: hydroxypyruvate decarboxylase
Reaction: hydroxypyruvate = glycolaldehyde + CO2
Other name(s): hydroxypyruvate carboxy-lyase
Systematic name: hydroxypyruvate carboxy-lyase (glycolaldehyde-forming)
References:
1.  Hedrick, J.L. and Sallach, H.J. The nonoxidative decarboxylation of hydroxypyruvate in mammalian systems. Arch. Biochem. Biophys. 105 (1964) 261–269. [PMID: 14186730]
[EC 4.1.1.40 created 1972]
 
 
EC 4.1.1.41      
Transferred entry: (S)-methylmalonyl-CoA decarboxylase. Now EC 7.2.4.3, (S)-methylmalonyl-CoA decarboxylase
[EC 4.1.1.41 created 1972, modified 1983, modified 1986, deleted 2018]
 
 
EC 4.1.1.42     
Accepted name: carnitine decarboxylase
Reaction: carnitine = 2-methylcholine + CO2
Other name(s): carnitine carboxy-lyase
Systematic name: carnitine carboxy-lyase (2-methylcholine-forming)
Comments: Requires ATP.
References:
1.  Khairallah, E.A. and Wolf, G. Carnitine decarboxylase. The conversion of carnitine to β-methylcholine. J. Biol. Chem. 242 (1967) 32–39. [PMID: 6016331]
[EC 4.1.1.42 created 1972]
 
 
EC 4.1.1.43     
Accepted name: phenylpyruvate decarboxylase
Reaction: phenylpyruvate = phenylacetaldehyde + CO2
Glossary: phenylpyruvate = 3-phenyl-2-oxopropanoate
Other name(s): phenylpyruvate carboxy-lyase; phenylpyruvate carboxy-lyase (phenylacetaldehyde-forming)
Systematic name: 3-phenyl-2-oxopropanoate carboxy-lyase (phenylacetaldehyde-forming)
Comments: The enzyme from the bacterium Azospirillum brasilense also acts on some other substrates, including (indol-3-yl)pyruvate, with much lower efficiency. However, it only possesses classical Michaelis-Menten kinetics with phenylpyruvate. Aliphatic 2-oxo acids longer that 2-oxohexanoate are not substrates. cf. EC 4.1.1.74, indolepyruvate decarboxylase.
References:
1.  Asakawa, T., Wada, H. and Yamano, T. Enzymatic conversion of phenylpyruvate to phenylacetate. Biochim. Biophys. Acta 170 (1968) 375–391. [PMID: 4303395]
2.  Spaepen, S., Versees, W., Gocke, D., Pohl, M., Steyaert, J. and Vanderleyden, J. Characterization of phenylpyruvate decarboxylase, involved in auxin production of Azospirillum brasilense. J. Bacteriol. 189 (2007) 7626–7633. [PMID: 17766418]
[EC 4.1.1.43 created 1972]
 
 
EC 4.1.1.44     
Accepted name: 4-carboxymuconolactone decarboxylase
Reaction: (R)-2-carboxy-2,5-dihydro-5-oxofuran-2-acetate = 4,5-dihydro-5-oxofuran-2-acetate + CO2
Glossary: 4-carboxymuconolactone = 2-carboxy-2,5-dihydro-5-oxofuran-2-acetate
Other name(s): γ-4-carboxymuconolactone decarboxylase; 4-carboxymuconolactone carboxy-lyase; 2-carboxy-2,5-dihydro-5-oxofuran-2-acetate carboxy-lyase (4,5-dihydro-5-oxofuran-2-acetate-forming)
Systematic name: (R)-2-carboxy-2,5-dihydro-5-oxofuran-2-acetate carboxy-lyase (4,5-dihydro-5-oxofuran-2-acetate-forming)
References:
1.  Ornston, L.N. The conversion of catechol and protocatechuate to β-ketoadipate by Pseudomonas putida. 3. Enzymes of the catechol pathway. J. Biol. Chem. 241 (1966) 3795–3799. [PMID: 5330966]
2.  Ornston, L.N. Conversion of catechol and protocatechuate to β-ketoadipate (Pseudomonas putida). Methods Enzymol. 17A (1970) 529–549.
[EC 4.1.1.44 created 1972]
 
 
EC 4.1.1.45     
Accepted name: aminocarboxymuconate-semialdehyde decarboxylase
Reaction: 2-amino-3-(3-oxoprop-1-en-1-yl)but-2-enedioate = 2-aminomuconate semialdehyde + CO2
Glossary: aminocarboxymuconate semialdehyde = 2-amino-3-(3-oxoprop-1-en-1-yl)but-2-enedioate
Other name(s): picolinic acid carboxylase; picolinic acid decarboxylase; α-amino-β-carboxymuconate-ε-semialdehade decarboxylase; α-amino-β-carboxymuconate-ε-semialdehyde β-decarboxylase; 2-amino-3-(3-oxoprop-2-enyl)but-2-enedioate carboxy-lyase; 2-amino-3-(3-oxoprop-1-en-1-yl)but-2-enedioate carboxy-lyase
Systematic name: 2-amino-3-(3-oxoprop-1-en-1-yl)but-2-enedioate carboxy-lyase (2-aminomuconate-semialdehyde-forming)
Comments: Product rearranges non-enzymically to picolinate.
References:
1.  Ichiyama, A., Nakamura, S., Kawai, H., Honjo, T., Nishizuka, Y., Hayaishi, O. and Senoh, S. Studies on the metabolism of the benzene ring of tryptophan in mammalian tissues. II. Enzymic formation of α-aminomuconic acid from 3-hydroxyanthranilic acid. J. Biol. Chem. 240 (1965) 740–749. [PMID: 14275130]
[EC 4.1.1.45 created 1972]
 
 
EC 4.1.1.46     
Accepted name: o-pyrocatechuate decarboxylase
Reaction: 2,3-dihydroxybenzoate = catechol + CO2
Other name(s): 2,3-dihydroxybenzoate carboxy-lyase
Systematic name: 2,3-dihydroxybenzoate carboxy-lyase (catechol-forming)
References:
1.  Subba Rao, P.V., Moore, K., Towers, G.H.N. O-Pyrocatechiuc acid carboxy-lyase from Aspergillus niger. Arch. Biochem. Biophys. 122 (1967) 466–473. [PMID: 6066253]
[EC 4.1.1.46 created 1972]
 
 
EC 4.1.1.47     
Accepted name: tartronate-semialdehyde synthase
Reaction: 2 glyoxylate = 2-hydroxy-3-oxopropanoate + CO2
Glossary: 2-hydroxy-3-oxopropanoate = tartronate semialdehyde
Other name(s): tartronate semialdehyde carboxylase; glyoxylate carbo-ligase; glyoxylic carbo-ligase; hydroxymalonic semialdehyde carboxylase; tartronic semialdehyde carboxylase; glyoxalate carboligase; glyoxylate carboxy-lyase (dimerizing); glyoxylate carboxy-lyase (dimerizing; tartronate-semialdehyde-forming)
Systematic name: glyoxylate carboxy-lyase (dimerizing; 2-hydroxy-3-oxopropanoate-forming)
Comments: A flavoprotein.
References:
1.  Gupta, N.K. and Vennesland, B. Glyoxylate carboligase of Escherichia coli: a flavoprotein. J. Biol. Chem. 239 (1964) 3787–3789. [PMID: 14257608]
2.  Krakow, G. and Barkulis, S.S. Conversion of glyoxylate to hydroxypyruvate by extracts of Escherichia coli. Biochim. Biophys. Acta 21 (1956) 593–594. [PMID: 13363977]
[EC 4.1.1.47 created 1972]
 
 
EC 4.1.1.48     
Accepted name: indole-3-glycerol-phosphate synthase
Reaction: 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate = 1-C-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O
Other name(s): indoleglycerol phosphate synthetase; indoleglycerol phosphate synthase; indole-3-glycerophosphate synthase; 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose-5-phosphate carboxy-lyase (cyclizing)
Systematic name: 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose-5-phosphate carboxy-lyase [cyclizing; 1-C-(indol-3-yl)glycerol-3-phosphate-forming]
Comments: In some organisms, this enzyme is part of a multifunctional protein, together with one or more other components of the system for the biosynthesis of tryptophan [EC 2.4.2.18 (anthranilate phosphoribosyltransferase), EC 4.1.3.27 (anthranilate synthase), EC 4.2.1.20 (tryptophan synthase) and EC 5.3.1.24 (phosphoribosylanthranilate isomerase)].
References:
1.  Creighton, T.E. and Yanofsky, C. Indole-3-glycerol phosphate synthetase of Escherichia coli, an enzyme of the tryptophan operon. J. Biol. Chem. 241 (1966) 4616–4624. [PMID: 5332729]
2.  Creighton, T.E. and Yanofsky, C. Chorismate to tryptophan (Escherichia coli) - anthranilate synthetase, PR transferase, PRA isomerase, InGP synthetase, tryptophan synthetase. Methods Enzymol. 17A (1970) 365–380.
3.  Hütter, R., Niederberger, P. and DeMoss, J.A. Tryptophan synthetic genes in eukaryotic microorganisms. Annu. Rev. Microbiol. 40 (1986) 55–77. [PMID: 3535653]
[EC 4.1.1.48 created 1972]
 
 
EC 4.1.1.49     
Accepted name: phosphoenolpyruvate carboxykinase (ATP)
Reaction: ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO2
Other name(s): phosphopyruvate carboxylase (ATP); phosphoenolpyruvate carboxylase (ambiguous); phosphoenolpyruvate carboxykinase (ambiguous); phosphopyruvate carboxykinase (adenosine triphosphate); PEP carboxylase (ambiguous); PEP carboxykinase (ambiguous); PEPCK (ATP); PEPK; PEPCK; phosphoenolpyruvic carboxylase (ambiguous); phosphoenolpyruvic carboxykinase (ambiguous); phosphoenolpyruvate carboxylase (ATP); phosphopyruvate carboxykinase (ambiguous); ATP:oxaloacetate carboxy-lyase (transphosphorylating)
Systematic name: ATP:oxaloacetate carboxy-lyase (transphosphorylating; phosphoenolpyruvate-forming)
References:
1.  Cannata, J.J.B. Phosphoenolpyruvate carboxykinase from bakers' yeast. Isolation of the enzyme and study of its physical properties. J. Biol. Chem. 245 (1970) 792–798. [PMID: 5416663]
2.  Cannata, J.J.B. and Stoppani, A.O.M. Phosphopyruvate carboxylase from baker's yeast. I. Isolation, purification, and characterization. J. Biol. Chem. 238 (1963) 1196–1207. [PMID: 14018315]
3.  Cannata, J.J.B. and Stoppani, A.O.M. Phosphopyruvate carboxylase from baker's yeast. II. Properties of enzyme. J. Biol. Chem. 238 (1963) 1208–1212. [PMID: 14018316]
[EC 4.1.1.49 created 1972]
 
 
EC 4.1.1.50     
Accepted name: adenosylmethionine decarboxylase
Reaction: S-adenosyl-L-methionine = S-adenosyl 3-(methylsulfanyl)propylamine + CO2
Glossary: S-adenosyl 3-(methylsulfanyl)propylamine = (3-aminopropyl){[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}methylsulfonium
Other name(s): S-adenosylmethionine decarboxylase; S-adenosyl-L-methionine decarboxylase; S-adenosyl-L-methionine carboxy-lyase; S-adenosyl-L-methionine carboxy-lyase [(5-deoxy-5-adenosyl)(3-aminopropyl)methylsulfonium-salt-forming]
Systematic name: S-adenosyl-L-methionine carboxy-lyase [S-adenosyl 3-(methylsulfanyl)propylamine-forming]
Comments: The Escherichia coli enzyme contains a pyruvoyl group.
References:
1.  Anton, D.L. and Kutny, R. Escherichia coli S-adenosylmethionine decarboxylase. Subunit structure, reductive amination, and NH2-terminal sequences. J. Biol. Chem. 262 (1987) 2817–2822. [PMID: 3546296]
2.  Tabor, C.W. Adenosylmethionine decarboxylase. Methods Enzymol. 5 (1962) 756–760.
[EC 4.1.1.50 created 1972]
 
 
EC 4.1.1.51     
Accepted name: 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase
Reaction: 3-hydroxy-2-methylpyridine-4,5-dicarboxylate = 3-hydroxy-2-methylpyridine-5-carboxylate + CO2
Other name(s): 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-carboxy-lyase
Systematic name: 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-carboxy-lyase (3-hydroxy-2-methylpyridine-5-carboxylate-forming)
References:
1.  Snell, E.E., Smucker, A.A., Ringelmann, E. and Lynen, F. Die bakterielle Oxydation des Vitamin B6. IV. Die enzymatische Decarboxylierung von 2-Methyl-3-hydroxypyridine-4,5-dicarbonsäure. Biochem. Z. 341 (1964) 109–119. [PMID: 14339645]
[EC 4.1.1.51 created 1972]
 
 
EC 4.1.1.52     
Accepted name: 6-methylsalicylate decarboxylase
Reaction: 6-methylsalicylate = 3-methylphenol + CO2
Glossary: 3-methylphenol = 3-cresol = m-cresol
Other name(s): 6-methylsalicylic acid (2,6-cresotic acid) decarboxylase; 6-MSA decarboxylase; 6-methylsalicylate carboxy-lyase
Systematic name: 6-methylsalicylate carboxy-lyase (3-methylphenol-forming)
References:
1.  Light, R.J. 6-Methylsalicylic acid decarboxylase from Penicillium patulum. Biochim. Biophys. Acta 191 (1969) 430–438. [PMID: 5354271]
2.  Vogel, G. and Lynen, F. 6-Methylsalicylsäure-Decarboxylase. Naturwissenschaften 57 (1970) 664.
[EC 4.1.1.52 created 1972, modified 2011]
 
 
EC 4.1.1.53     
Accepted name: phenylalanine decarboxylase
Reaction: L-phenylalanine = phenylethylamine + CO2
Other name(s): L-phenylalanine decarboxylase; aromatic L-amino acid decarboxylase (ambiguous); L-phenylalanine carboxy-lyase
Systematic name: L-phenylalanine carboxy-lyase (phenylethylamine-forming)
Comments: A pyridoxal-phosphate protein. Also acts on tyrosine and other aromatic amino acids.
References:
1.  Lovenberg, W., Weissbach, H. and Udenfriend, S. Aromatic L-amino acid decarboxylase. J. Biol. Chem. 237 (1962) 89–93. [PMID: 14466899]
2.  Schulz, A.R. and Oliner, L. The possible role of thyroid aromatic amino acid decarboxylase in thyroxine biosynthesis. Life Sci. 6 (1967) 873–880. [PMID: 6034195]
[EC 4.1.1.53 created 1972]
 
 
EC 4.1.1.54     
Accepted name: dihydroxyfumarate decarboxylase
Reaction: dihydroxyfumarate = 2-hydroxy-3-oxopropanoate + CO2
Glossary: 2-hydroxy-3-oxopropanoate = tartronate semialdehyde
Other name(s): dihydroxyfumarate carboxy-lyase; dihydroxyfumarate carboxy-lyase (tartronate-semialdehyde-forming)
Systematic name: dihydroxyfumarate carboxy-lyase (2-hydroxy-3-oxopropanoate-forming)
References:
1.  Fukumaga, K. Metabolism of dihydroxyfumarate, hydroxypyruvate, and their related compounds. I. Enzymic formation of xylulose in liver. J. Biochem. (Tokyo) 47 (1960) 741–754.
[EC 4.1.1.54 created 1972]
 
 
EC 4.1.1.55     
Accepted name: 4,5-dihydroxyphthalate decarboxylase
Reaction: 4,5-dihydroxyphthalate = 3,4-dihydroxybenzoate + CO2
Other name(s): 4,5-dihydroxyphthalate carboxy-lyase
Systematic name: 4,5-dihydroxyphthalate carboxy-lyase (3,4-dihydroxybenzoate-forming)
References:
1.  Ribbons, D.W. and Evans, W.C. Oxidative metabolism of phthalic acid by soil pseudomonads. Biochem. J. 76 (1966) 310–318. [PMID: 16748829]
[EC 4.1.1.55 created 1972]
 
 
EC 4.1.1.56     
Accepted name: 3-oxolaurate decarboxylase
Reaction: 3-oxododecanoate = 2-undecanone + CO2
Other name(s): β-ketolaurate decarboxylase; β-ketoacyl decarboxylase; 3-oxododecanoate carboxy-lyase
Systematic name: 3-oxododecanoate carboxy-lyase (2-undecanone-forming)
Comments: Also decarboxylates other C14 to C16 oxo acids.
References:
1.  Franke, W., Platzeck, A. and Eichhorn, G. [On the knowledge of fatty acid catabolism by mold fungi. III. On a decarboxylase for average β-ketomonocarbonic acids (β-ketolaurate decarboxylase)] Arch. Mikrobiol. 40 (1961) 73–93. [PMID: 13701396]
[EC 4.1.1.56 created 1972]
 
 
EC 4.1.1.57     
Accepted name: methionine decarboxylase
Reaction: L-methionine = 3-(methylsulfanyl)propanamine + CO2
Other name(s): L-methionine decarboxylase; L-methionine carboxy-lyase; L-methionine carboxy-lyase (3-methylthiopropanamine-forming)
Systematic name: L-methionine carboxy-lyase [3-(methylsulfanyl)propanamine-forming]
References:
1.  Hagion, H. and Nakayama, K. Amino acid metabolism in microorganisms. Part IV. L-Methionine decarboxylase produced by Streptomyces strain. Agric. Biol. Chem. 32 (1968) 727–733.
[EC 4.1.1.57 created 1972]
 
 
EC 4.1.1.58     
Accepted name: orsellinate decarboxylase
Reaction: orsellinate = orcinol + CO2
Glossary: orsellinate = 2,4-dihydroxy-6-methylbenzoate
Other name(s): orsellinate carboxy-lyase
Systematic name: 2,4-dihydroxy-6-methylbenzoate carboxy-lyase (orcinol-forming)
References:
1.  Pettersson, G. An orsellinic acid decarboxylase isolated from Gliocladium roseum. Acta Chem. Scand. 19 (1965) 2013–2021.
[EC 4.1.1.58 created 1972]
 
 
EC 4.1.1.59     
Accepted name: gallate decarboxylase
Reaction: 3,4,5-trihydroxybenzoate = 1,2,3-trihydroxybenzene + CO2
Glossary: 3,4,5-trihydroxybenzoate = gallate
1,2,3-trihydroxybenzene = pyrogallol
Other name(s): gallic acid decarboxylase; gallate carboxy-lyase; 3,4,5-trihydroxybenzoate carboxy-lyase (pyrogallol-forming)
Systematic name: 3,4,5-trihydroxybenzoate carboxy-lyase (1,2,3-trihydroxybenzene-forming)
References:
1.  Grant, D.J.W. and Patel, J.C. Non-oxidative decarboxylation of p-hydroxybenzoic acid, gentisic acid, protocatechuic acid, and gallic acid by Klebsiella aerogenes (Aerobacter aerogenes). J. Microbiol. Serol. 35 (1969) 325–343. [PMID: 5309907]
2.  Zeida, M., Wieser, M., Yoshida, T., Sugio, T. and Nagasawa, T. Purification and characterization of gallic acid decarboxylase from Pantoea agglomerans T7. Appl. Environ. Microbiol. 64 (1998) 4743–4747. [PMID: 9835557]
3.  Jimenez, N., Curiel, J.A., Reveron, I., de Las Rivas, B. and Munoz, R. Uncovering the Lactobacillus plantarum WCFS1 gallate decarboxylase involved in tannin degradation. Appl. Environ. Microbiol. 79 (2013) 4253–4263. [PMID: 23645198]
[EC 4.1.1.59 created 1972]
 
 
EC 4.1.1.60     
Accepted name: stipitatonate decarboxylase
Reaction: stipitatonate = stipitatate + CO2
Glossary: stipitatonate = 4,7-dihydroxy-1H-cyclohepta[c]furan-1,3,6-trione
stipitatate = 3,6-dihydroxy-5-oxocyclohepta-1,3,6-triene-1-carboxylate
Other name(s): stipitatonate carboxy-lyase (decyclizing); stipitatonate carboxy-lyase (decyclizing, stipitatate-forming)
Systematic name: stipitatonate carboxy-lyase (ring-opening, stipitatate-forming)
References:
1.  Bentley, R. and Thiessen, C.P. Biosynthesis of tropolones in Penicillium stipitatum. V. Preparation and properties of stipitatonic acid decarboxylase. J. Biol. Chem. 238 (1963) 3811–3816. [PMID: 14109225]
[EC 4.1.1.60 created 1972]
 
 
EC 4.1.1.61     
Accepted name: 4-hydroxybenzoate decarboxylase
Reaction: 4-hydroxybenzoate = phenol + CO2
Other name(s): p-hydroxybenzoate decarboxylase; 4-hydroxybenzoate carboxy-lyase
Systematic name: 4-hydroxybenzoate carboxy-lyase (phenol-forming)
References:
1.  Grant, D.J.W. and Patel, J.C. Non-oxidative decarboxylation of p-hydroxybenzoic acid, gentisic acid, protocatechuic acid, and gallic acid by Klebsiella aerogenes (Aerobacter aerogenes). J. Microbiol. Serol. 35 (1969) 325–343. [PMID: 5309907]
2.  Tschech, A. and Fuchs, G. Anaerobic degradation of phenol via carboxylation to 4-hydroxybenzoate - in vitro study of isotope exchange between (CO2)-C-14 and 4-hydroxybenzoate. Arch. Microbiol. 152 (1989) 594–599.
[EC 4.1.1.61 created 1972]
 
 
EC 4.1.1.62     
Accepted name: gentisate decarboxylase
Reaction: 2,5-dihydroxybenzoate = hydroquinone + CO2
Glossary: gentisate = 2,5-dihydroxybenzoate
Other name(s): 2,5-dihydroxybenzoate decarboxylase; gentisate carboxy-lyase
Systematic name: 2,5-dihydroxybenzoate carboxy-lyase (hydroquinone-forming)
References:
1.  Grant, D.J.W. and Patel, J.C. Non-oxidative decarboxylation of p-hydroxybenzoic acid, gentisic acid, protocatechuic acid, and gallic acid by Klebsiella aerogenes (Aerobacter aerogenes). J. Microbiol. Serol. 35 (1969) 325–343. [PMID: 5309907]
[EC 4.1.1.62 created 1972]
 
 
EC 4.1.1.63     
Accepted name: protocatechuate decarboxylase
Reaction: 3,4-dihydroxybenzoate = catechol + CO2
Glossary: protocatechuate = 3,4-dihydroxybenzoate
Other name(s): 3,4-dihydrobenzoate decarboxylase; protocatechuate carboxy-lyase
Systematic name: 3,4-dihydroxybenzoate carboxy-lyase (catechol-forming)
References:
1.  Grant, D.J.W. and Patel, J.C. Non-oxidative decarboxylation of p-hydroxybenzoic acid, gentisic acid, protocatechuic acid, and gallic acid by Klebsiella aerogenes (Aerobacter aerogenes). J. Microbiol. Serol. 35 (1969) 325–343. [PMID: 5309907]
[EC 4.1.1.63 created 1972]
 
 
EC 4.1.1.64     
Accepted name: 2,2-dialkylglycine decarboxylase (pyruvate)
Reaction: 2,2-dialkylglycine + pyruvate = dialkyl ketone + CO2 + L-alanine
Other name(s): dialkyl amino acid (pyruvate) decarboxylase; α-dialkyl amino acid transaminase; 2,2-dialkyl-2-amino acid-pyruvate aminotransferase; L-alanine-α-ketobutyrate aminotransferase; dialkylamino-acid decarboxylase (pyruvate); 2,2-dialkylglycine carboxy-lyase (amino-transferring)
Systematic name: 2,2-dialkylglycine carboxy-lyase (amino-transferring; L-alanine-forming)
Comments: A pyridoxal-phosphate protein. Acts on 2-amino-2-methylpropanoate (i.e. 2-methylalanine), 2-amino-2-methylbutanoate and 1-aminocyclopentanecarboxylate.
References:
1.  Bailey, G.B. and Dempsey, W.B. Purification and properties of an α-dialkyl amino acid transaminase. Biochemistry 6 (1967) 1526–1533.
[EC 4.1.1.64 created 1972]
 
 
EC 4.1.1.65     
Accepted name: phosphatidylserine decarboxylase
Reaction: phosphatidyl-L-serine = phosphatidylethanolamine + CO2
Other name(s): PS decarboxylase; phosphatidyl-L-serine carboxy-lyase
Systematic name: phosphatidyl-L-serine carboxy-lyase (phosphatidylethanolamine-forming)
Comments: A pyridoxal-phosphate protein. In Escherichia coli, the prosthetic group is a pyruvoyl group.
References:
1.  Kanfer, J. and Kennedy, E.P. Metabolism and function of bacterial lipids. II. Biosynthesis of phospholipids in Escherichia coli. J. Biol. Chem. 239 (1964) 1720–1726. [PMID: 14213340]
2.  Satre, M. and Kennedy, E.P. Identification of bound pyruvate essential for the activity of phosphatidylserine decarboxylase of Escherichia coli. J. Biol. Chem. 253 (1978) 479–483. [PMID: 338609]
[EC 4.1.1.65 created 1976]
 
 
EC 4.1.1.66     
Accepted name: uracil-5-carboxylate decarboxylase
Reaction: uracil 5-carboxylate = uracil + CO2
Other name(s): uracil-5-carboxylic acid decarboxylase; uracil-5-carboxylate carboxy-lyase
Systematic name: uracil-5-carboxylate carboxy-lyase (uracil-forming)
References:
1.  Palmatier, R.D., McCroskey, R.P. and Abbott, M.T. The enzymatic conversion of uracil 5-carboxylic acid to uracil and carbon dioxide. J. Biol. Chem. 245 (1970) 6706–6710. [PMID: 5482775]
[EC 4.1.1.66 created 1976]
 
 
EC 4.1.1.67     
Accepted name: UDP-galacturonate decarboxylase
Reaction: UDP-D-galacturonate = UDP-L-arabinose + CO2
Other name(s): UDP-galacturonic acid decarboxylase; UDPGalUA carboxy lyase; UDP-D-galacturonate carboxy-lyase
Systematic name: UDP-D-galacturonate carboxy-lyase (UDP-L-arabinose-forming)
References:
1.  Fan, D.-F. and Feingold, D.S. UDPgalacturonic acid decarboxylase from Ampullariella digitata. Methods Enzymol. 28B (1972) 438–439.
[EC 4.1.1.67 created 1984]
 
 
EC 4.1.1.68     
Accepted name: 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase
Reaction: (3E,5R)-5-carboxy-2-oxohept-3-enedioate = (4Z)-2-oxohept-4-enedioate + CO2 (overall reaction)
(1a) (3E,5R)-5-carboxy-2-oxohept-3-enedioate = (2Z,4Z)-2-hydroxyhepta-2,4-dienedioate + CO2
(1b) (2Z,4Z)-2-hydroxyhepta-2,4-dienedioate = (4Z)-2-oxohept-4-enedioate
Glossary: 5-carboxy-2-oxohept-3-enedioate = 5-oxopent-3-ene-1,2,5-tricarboxylate
Other name(s): 5-carboxymethyl-2-oxo-hex-3-ene-1,6-dioate decarboxylase; 5-oxopent-3-ene-1,2,5-tricarboxylate carboxy-lyase; 5-oxopent-3-ene-1,2,5-tricarboxylate carboxy-lyase (2-oxohept-3-enedioate-forming)
Systematic name: (3E,5R)-5-carboxy-2-oxohept-3-enedioate carboxy-lyase [(4Z)-2-oxohept-4-enedioate-forming]
Comments: Requires Mg2+ [2,3]. Part of the 4-hydroxyphenylacetate degradation pathway in Escherichia coli.
References:
1.  Garrido-Pertierra, A. and Cooper, R.A. Identification and purification of distinct isomerase and decarboxylase enzymes involved in the 4-hydroxyphenylacetate pathway of Escherichia coli. Eur. J. Biochem. 117 (1981) 581–584. [PMID: 7026235]
2.  Johnson, W.H., Jr., Hajipour, G. and Whitman, C.P. Characterization of a dienol intermediate in the 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dioate decarboxylase reaction. J. Am. Chem. Soc. 114 (1992) 11001–11003.
3.  Johnson, W.H., Jr., Hajipour, G. and Whitman, C.P. Stereochemical studies of 5-(carboxymethyl)-2-hydroxymuconate isomerase and 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dioate decarboxylase from Escherichia coli C: mechanistic and evolutionary implications. J. Am. Chem. Soc. 117 (1995) 8719–8726.
[EC 4.1.1.68 created 1984]
 
 
EC 4.1.1.69     
Accepted name: 3,4-dihydroxyphthalate decarboxylase
Reaction: 3,4-dihydroxyphthalate = 3,4-dihydroxybenzoate + CO2
Other name(s): 3,4-dihydroxyphthalate carboxy-lyase
Systematic name: 3,4-dihydroxyphthalate carboxy-lyase (3,4-dihydroxybenzoate-forming)
References:
1.  Eaton, R.W. and Ribbons, D.W. Metabolism of dibutylphthalate and phthalate by Micrococcus sp. strain 12B. J. Gen. Microbiol. 151 (1982) 48–57. [PMID: 7085570]
[EC 4.1.1.69 created 1986]
 
 
EC 4.1.1.70      
Transferred entry: glutaconyl-CoA decarboxylase. Now EC 7.2.4.5, glutaconyl-CoA decarboxylase
[EC 4.1.1.70 created 1986, modified 2003, deleted 2019]
 
 
EC 4.1.1.71     
Accepted name: 2-oxoglutarate decarboxylase
Reaction: 2-oxoglutarate = succinate semialdehyde + CO2
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): oxoglutarate decarboxylase; α-ketoglutarate decarboxylase; α-ketoglutaric decarboxylase; pre-2-oxoglutarate decarboxylase; 2-oxoglutarate carboxy-lyase
Systematic name: 2-oxoglutarate carboxy-lyase (succinate-semialdehyde-forming)
Comments: Requires thiamine diphosphate. Highly specific.
References:
1.  Shigeoka, S., Onishi, T., Maeda, K., Nakano, Y. and Kitaoka, S. Occurrence of thiamin pyrophosphate-dependent 2-oxoglutarate decarboxylase in mitochondria of Euglena gracilis. FEBS Lett. 195 (1986) 43–47.
[EC 4.1.1.71 created 1989]
 
 
EC 4.1.1.72     
Accepted name: branched-chain-2-oxoacid decarboxylase
Reaction: (3S)-3-methyl-2-oxopentanoate = 2-methylbutanal + CO2
Other name(s): branched-chain oxo acid decarboxylase; branched-chain α-keto acid decarboxylase; branched-chain keto acid decarboxylase; BCKA; (3S)-3-methyl-2-oxopentanoate carboxy-lyase
Systematic name: (3S)-3-methyl-2-oxopentanoate carboxy-lyase (2-methylbutanal-forming)
Comments: Acts on a number of 2-oxo acids, with a high affinity towards branched-chain substrates. The aldehyde formed may be enzyme-bound, and may be an intermediate in the bacterial system for the biosynthesis of branched-chain fatty acids.
References:
1.  Oku, H. and Kaneda, T. Biosynthesis of branched-chain fatty acids in Bacillus subtilis. A decarboxylase is essential for branched-chain fatty acid synthetase. J. Biol. Chem. 263 (1988) 18386–18396. [PMID: 3142877]
2.  de la Plaza, M., Fernandez de Palencia, P., Pelaez, C. and Requena, T. Biochemical and molecular characterization of α-ketoisovalerate decarboxylase, an enzyme involved in the formation of aldehydes from amino acids by Lactococcus lactis. FEMS Microbiol. Lett. 238 (2004) 367–374. [PMID: 15358422]
3.  Smit, B.A., van Hylckama Vlieg, J.E., Engels, W.J., Meijer, L., Wouters, J.T. and Smit, G. Identification, cloning, and characterization of a Lactococcus lactis branched-chain α-keto acid decarboxylase involved in flavor formation. Appl. Environ. Microbiol. 71 (2005) 303–311. [PMID: 15640202]
[EC 4.1.1.72 created 1990]
 
 
EC 4.1.1.73     
Accepted name: tartrate decarboxylase
Reaction: (R,R)-tartrate = D-glycerate + CO2
Other name(s): (R,R)-tartrate carboxy-lyase
Systematic name: (R,R)-tartrate carboxy-lyase (D-glycerate-forming)
References:
1.  Furuyoshi, S., Kawabata, N., Tanaka, H. and Soda, K. Enzymatic production of D-glycerate from L-tartrate. Agric. Biol. Chem. 53 (1989) 2101–2105.
[EC 4.1.1.73 created 1992]
 
 
EC 4.1.1.74     
Accepted name: indolepyruvate decarboxylase
Reaction: 3-(indol-3-yl)pyruvate = 2-(indol-3-yl)acetaldehyde + CO2
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): indol-3-yl-pyruvate carboxy-lyase; 3-(indol-3-yl)pyruvate carboxy-lyase
Systematic name: 3-(indol-3-yl)pyruvate carboxy-lyase [(2-indol-3-yl)acetaldehyde-forming]
Comments: Thiamine diphosphate- and Mg2+-dependent. More specific than EC 4.1.1.1 pyruvate decarboxylase
References:
1.  Koga, J. Structure and function of indolepyruvate decarboxylase, a key enzyme in indole-3-pyruvic acid biosynthesis. Biochim. Biophys. Acta 1249 (1995) 1–13. [PMID: 7766676]
[EC 4.1.1.74 created 1999]
 
 
EC 4.1.1.75     
Accepted name: 5-guanidino-2-oxopentanoate decarboxylase
Reaction: 5-guanidino-2-oxopentanoate = 4-guanidinobutanal + CO2
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): α-ketoarginine decarboxylase; 2-oxo-5-guanidinopentanoate carboxy-lyase
Systematic name: 5-guanidino-2-oxopentanoate carboxy-lyase (4-guanidinobutanal-forming)
Comments: Enzyme activity is dependent on the presence of thiamine diphosphate and a divalent cation.
References:
1.  Vanderbilt, A.S., Gaby, N.S., Rodwell, V.W. Intermediates and enzymes between α-ketoarginine and γ-guanidinobutyrate in the L-arginine catabolic pathway of Pseudomonas putida. J. Biol. Chem. 250 (1975) 5322–5329. [PMID: 237915]
[EC 4.1.1.75 created 1999]
 
 
EC 4.1.1.76     
Accepted name: arylmalonate decarboxylase
Reaction: 2-aryl-2-methylmalonate = 2-arylpropanoate + CO2
Other name(s): AMDASE; 2-aryl-2-methylmalonate carboxy-lyase; 2-aryl-2-methylmalonate carboxy-lyase (2-arylpropionate-forming)
Systematic name: 2-aryl-2-methylmalonate carboxy-lyase (2-arylpropanoate-forming)
References:
1.  Miyamoto, K., Ohta, H. Cloning and heterologous expression of a novel arylmalonate decarboxylase gene from Alcaligenes bronchisepticus KU 1201. Appl. Microbiol. Biotechnol. 38 (1992) 234–238. [PMID: 1369144]
[EC 4.1.1.76 created 1999]
 
 
EC 4.1.1.77     
Accepted name: 2-oxo-3-hexenedioate decarboxylase
Reaction: (3E)-2-oxohex-3-enedioate = 2-oxopent-4-enoate + CO2
Other name(s): 4-oxalocrotonate carboxy-lyase (misleading); 4-oxalocrotonate decarboxylase (misleading); cnbF (gene name); praD (gene name); amnE (gene name); nbaG (gene name); xylI (gene name)
Systematic name: (3E)-2-oxohex-3-enedioate carboxy-lyase (2-oxopent-4-enoate-forming)
Comments: Involved in the meta-cleavage pathway for the degradation of phenols, modified phenols and catechols. The enzyme has been reported to accept multiple tautomeric forms [1-4]. However, careful analysis of the stability of the different tautomers, as well as characterization of the enzyme that produces its substrate, EC 5.3.2.6, 2-hydroxymuconate tautomerase, showed that the actual substrate for the enzyme is (3E)-2-oxohex-3-enedioate [4].
References:
1.  Shingler, V., Marklund, U., Powlowski, J. Nucleotide sequence and functional analysis of the complete phenol/3,4-dimethylphenol catabolic pathway of Pseudomonas sp. strain CF600. J. Bacteriol. 174 (1992) 711–724. [PMID: 1732207]
2.  Takenaka, S., Murakami, S., Shinke, R. and Aoki, K. Metabolism of 2-aminophenol by Pseudomonas sp. AP-3: modified meta-cleavage pathway. Arch. Microbiol. 170 (1998) 132–137. [PMID: 9683650]
3.  Stanley, T.M., Johnson, W.H., Jr., Burks, E.A., Whitman, C.P., Hwang, C.C. and Cook, P.F. Expression and stereochemical and isotope effect studies of active 4-oxalocrotonate decarboxylase. Biochemistry 39 (2000) 718–726. [PMID: 10651637]
4.  Wang, S.C., Johnson, W.H., Jr., Czerwinski, R.M., Stamps, S.L. and Whitman, C.P. Kinetic and stereochemical analysis of YwhB, a 4-oxalocrotonate tautomerase homologue in Bacillus subtilis: mechanistic implications for the YwhB- and 4-oxalocrotonate tautomerase-catalyzed reactions. Biochemistry 46 (2007) 11919–11929. [PMID: 17902707]
5.  Kasai, D., Fujinami, T., Abe, T., Mase, K., Katayama, Y., Fukuda, M. and Masai, E. Uncovering the protocatechuate 2,3-cleavage pathway genes. J. Bacteriol. 191 (2009) 6758–6768. [PMID: 19717587]
[EC 4.1.1.77 created 1999, modified 2011, modified 2012]
 
 
EC 4.1.1.78     
Accepted name: acetylenedicarboxylate decarboxylase
Reaction: acetylenedicarboxylate + H2O = pyruvate + CO2
Other name(s): acetylenedicarboxylate hydratase; acetylenedicarboxylate hydrase; acetylenedicarboxylate carboxy-lyase
Systematic name: acetylenedicarboxylate carboxy-lyase (pyruvate-forming)
Comments: The mechanism appears to involve hydration of the acetylene and decarboxylation of the oxaloacetic acid formed, although free oxaloacetate is not an intermediate. It is thus analogous to EC 4.2.1.27 (acetylenecarboxylate hydratase) in its mechanism.
References:
1.  Yamada, E.W. and Jakoby, W.B. Enzymatic utilization of acetylenic compounds. I. An enzyme converting acetylenedicarboxylic acid to pyruvate. J. Biol. Chem. 233 (1958) 706–711. [PMID: 13575441]
[EC 4.1.1.78 created 1978 as EC 4.2.1.72, transferred 2000 to EC 4.1.1.78]
 
 
EC 4.1.1.79     
Accepted name: sulfopyruvate decarboxylase
Reaction: 3-sulfopyruvate = 2-sulfoacetaldehyde + CO2
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
2-sulfoacetaldehyde = 2-oxoethanesulfonate
Other name(s): sulfopyruvate carboxy-lyase
Systematic name: 3-sulfopyruvate carboxy-lyase (2-sulfoacetaldehyde-forming)
Comments: Requires thiamine diphosphate. Does not decarboxylate pyruvate or phosphonopyruvate. The enzyme appears to be oxygen-sensitive.
References:
1.  Graupner, M., Xu, H. and White, R.H. Identification of the gene encoding sulfopyruvate decarboxylase, an enzyme involved in biosynthesis of coenzyme M. J. Bacteriol. 182 (2000) 4862–4867. [PMID: 10940029]
[EC 4.1.1.79 created 2002]
 
 
EC 4.1.1.80     
Accepted name: 4-hydroxyphenylpyruvate decarboxylase
Reaction: 4-hydroxyphenylpyruvate = 4-hydroxyphenylacetaldehyde + CO2
Other name(s): 4-hydroxyphenylpyruvate carboxy-lyase
Systematic name: 4-hydroxyphenylpyruvate carboxy-lyase (4-hydroxyphenylacetaldehyde-forming)
Comments: Reacts with dopamine to give the benzylisoquinoline alkaloid skeleton.
References:
1.  Rueffer, M. and Zenk, M.H. Distant precursors of benzylisoquinoline alkaloids and their enzymatic formation. Z. Naturforsch. C: Biosci. 42 (1987) 319–332.
[EC 4.1.1.80 created 2002]
 
 
EC 4.1.1.81     
Accepted name: threonine-phosphate decarboxylase
Reaction: L-threonine O-3-phosphate = (R)-1-aminopropan-2-yl phosphate + CO2
Other name(s): L-threonine-O-3-phosphate decarboxylase; CobD; L-threonine-O-3-phosphate carboxy-lyase
Systematic name: L-threonine-O-3-phosphate carboxy-lyase [(R)-1-aminopropan-2-yl-phosphate-forming]
Comments: A pyridoxal-phosphate protein. This enzyme is unable to decarboxylate the D-isomer of threonine O-3-phosphate. The product of this reaction, (R)-1-aminopropan-2-yl phosphate, is the substrate of EC 6.3.1.10, adenosylcobinamide-phosphate synthase, which converts adenosylcobyric acid into adenosylcobinamide phosphate in the anaerobic cobalamin biosynthesis pathway.
References:
1.  Cheong, C.G., Bauer, C.B., Brushaber, K.R., Escalante-Semerena, J.C. and Rayment, I. Three-dimensional structure of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica. Biochemistry 41 (2002) 4798–4808. [PMID: 11939774]
2.  Brushaber, K.R., O'Toole, G.A. and Escalante-Semerena, J.C. CobD, a novel enzyme with L-threonine-O-3-phosphate decarboxylase activity, is responsible for the synthesis of (R)-1-amino-2-propanol O-2-phosphate, a proposed new intermediate in cobalamin biosynthesis in Salmonella typhimurium LT2. J. Biol. Chem. 273 (1998) 2684–2691. [PMID: 9446573]
3.  Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390–412. [PMID: 12195810]
[EC 4.1.1.81 created 2004]
 
 
EC 4.1.1.82     
Accepted name: phosphonopyruvate decarboxylase
Reaction: 3-phosphonopyruvate = 2-phosphonoacetaldehyde + CO2
Other name(s): 3-phosphonopyruvate carboxy-lyase
Systematic name: 3-phosphonopyruvate carboxy-lyase (2-phosphonoacetaldehyde-forming)
Comments: The enzyme catalyses a step in the biosynthetic pathway of 2-aminoethylphosphonate, a component of the capsular polysaccharide complex of Bacteroides fragilis. Requires thiamine diphosphate and Mg2+ as cofactors. The enzyme is activated by the divalent cations Mg2+, Ca2+ and Mn2+. Pyruvate and sulfopyruvate can also act as substrates, but more slowly. This enzyme drives the reaction catalysed by EC 5.4.2.9, phosphoenolpyruvate mutase, in the thermodynamically unfavourable direction of 3-phosphonopyruvate formation [2]. It is the initial step in all of the major biosynthetic pathways of phosphonate natural products [3].
References:
1.  Zhang, G., Dai, J., Lu, Z. and Dunaway-Mariano, D. The phosphonopyruvate decarboxylase from Bacteroides fragilis. J. Biol. Chem. 278 (2003) 41302–41308. [PMID: 12904299]
2.  Seidel, H.M. and Knowles, J.R. Interaction of inhibitors with phosphoenolpyruvate mutase: implications for the reaction mechanism and the nature of the active site. Biochemistry 33 (1994) 5641–5646. [PMID: 8180189]
3.  Nakashita, H., Watanabe, K., Hara, O., Hidaka, T. and Seto, H. Studies on the biosynthesis of bialaphos. Biochemical mechanism of C-P bond formation: discovery of phosphonopyruvate decarboxylase which catalyzes the formation of phosphonoacetaldehyde from phosphonopyruvate. J. Antibiot. (Tokyo) 50 (1997) 212–219. [PMID: 9127192]
[EC 4.1.1.82 created 2005]
 
 
EC 4.1.1.83     
Accepted name: 4-hydroxyphenylacetate decarboxylase
Reaction: (4-hydroxyphenyl)acetate + H+ = 4-methylphenol + CO2
Other name(s): p-hydroxyphenylacetate decarboxylase; p-Hpd; 4-Hpd; 4-hydroxyphenylacetate carboxy-lyase
Systematic name: (4-hydroxyphenyl)acetate carboxy-lyase (4-methylphenol-forming)
Comments: The enzyme, from the strict anaerobe Clostridium difficile, can also use (3,4-dihydroxyphenyl)acetate as a substrate, yielding 4-methylcatechol as a product. The enzyme is a glycyl radical enzyme.
References:
1.  D'Ari, L. and Barker, H.A. p-Cresol formation by cell-free extracts of Clostridium difficile. Arch. Microbiol. 143 (1985) 311–312. [PMID: 3938267]
2.  Selmer, T. and Andrei, P.I. p-Hydroxyphenylacetate decarboxylase from Clostridium difficile. A novel glycyl radical enzyme catalysing the formation of p-cresol. Eur. J. Biochem. 268 (2001) 1363–1372. [PMID: 11231288]
3.  Andrei, P.I., Pierik, A.J., Zauner, S., Andrei-Selmer, L.C. and Selmer, T. Subunit composition of the glycyl radical enzyme p-hydroxyphenylacetate decarboxylase. A small subunit, HpdC, is essential for catalytic activity. Eur. J. Biochem. 271 (2004) 2225–2230. [PMID: 15153112]
[EC 4.1.1.83 created 2005]
 
 
EC 4.1.1.84     
Accepted name: D-dopachrome decarboxylase
Reaction: D-dopachrome = 5,6-dihydroxyindole + CO2
Glossary: D-dopachrome = (2R)-5,6-dioxo-2,3,5,6-tetrahydro-1H-indole-2-carboxylate
Other name(s): phenylpyruvate tautomerase II; D-tautomerase; D-dopachrome tautomerase; D-dopachrome carboxy-lyase
Systematic name: D-dopachrome carboxy-lyase (5,6-dihydroxyindole-forming)
Comments: This enzyme is specific for D-dopachrome as substrate and belongs to the MIF (macrophage migration inhibitory factor) family of proteins. L-Dopachrome, L- or D-α-methyldopachrome and dopaminochrome do not act as substrates (see also EC 5.3.3.12, L-dopachrome isomerase)
References:
1.  Odh, G., Hindemith, A., Rosengren, A.M., Rosengren, E. and Rorsman, H. Isolation of a new tautomerase monitored by the conversion of D-dopachrome to 5,6-dihydroxyindole. Biochem. Biophys. Res. Commun. 197 (1993) 619–624. [PMID: 8267597]
2.  Yoshida, H., Nishihira, J., Suzuki, M. and Hikichi, K. NMR characterization of physicochemical properties of rat D-dopachrome tautomerase. Biochem. Mol. Biol. Int. 42 (1997) 891–899. [PMID: 9285056]
3.  Sugimoto, H., Taniguchi, M., Nakagawa, A., Tanaka, I., Suzuki, M. and Nishihira, J. Crystal structure of human D-dopachrome tautomerase, a homologue of macrophage migration inhibitory factor, at 1.54 Å resolution. Biochemistry 38 (1999) 3268–3279. [PMID: 10079069]
4.  Nishihira, J., Fujinaga, M., Kuriyama, T., Suzuki, M., Sugimoto, H., Nakagawa, A., Tanaka, I. and Sakai, M. Molecular cloning of human D-dopachrome tautomerase cDNA: N-terminal proline is essential for enzyme activation. Biochem. Biophys. Res. Commun. 243 (1998) 538–544. [PMID: 9480844]
[EC 4.1.1.84 created 2005]
 
 
EC 4.1.1.85     
Accepted name: 3-dehydro-L-gulonate-6-phosphate decarboxylase
Reaction: 3-dehydro-L-gulonate 6-phosphate + H+ = L-xylulose 5-phosphate + CO2
Other name(s): 3-keto-L-gulonate 6-phosphate decarboxylase; UlaD; SgaH; SgbH; KGPDC; 3-dehydro-L-gulonate-6-phosphate carboxy-lyase
Systematic name: 3-dehydro-L-gulonate-6-phosphate carboxy-lyase (L-xylulose-5-phosphate-forming)
Comments: Requires Mg2+. Along with EC 5.1.3.22, L-ribulose-5-phosphate 3-epimerase, this enzyme is involved in a pathway for the utilization of L-ascorbate by Escherichia coli.
References:
1.  Yew, W.S. and Gerlt, J.A. Utilization of L-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operons. J. Bacteriol. 184 (2002) 302–306. [PMID: 11741871]
2.  Wise, E., Yew, W.S., Babbitt, P.C., Gerlt, J.A. and Rayment, I. Homologous 8-barrel enzymes that catalyze unrelated reactions: orotidine 5′-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase. Biochemistry 41 (2002) 3861–3869. [PMID: 11900527]
[EC 4.1.1.85 created 2005]
 
 
EC 4.1.1.86     
Accepted name: diaminobutyrate decarboxylase
Reaction: L-2,4-diaminobutanoate = propane-1,3-diamine + CO2
Other name(s): DABA DC; L-2,4-diaminobutyrate decarboxylase; L-2,4-diaminobutanoate carboxy-lyase
Systematic name: L-2,4-diaminobutanoate carboxy-lyase (propane-1,3-diamine-forming)
Comments: A pyridoxal-phosphate protein that requires a divalent cation for activity [1]. N4-Acetyl-L-2,4-diaminobutanoate, 2,3-diaminopropanoate, ornithine and lysine are not substrates. Found in the proteobacteria Haemophilus influenzae and Acinetobacter baumannii. In the latter, this enzyme is cotranscribed with the dat gene that encodes EC 2.6.1.76, diaminobutyrate—2-oxoglutarate transaminase, which can supply the substrate for this enzyme.
References:
1.  Yamamoto, S., Tsuzaki, Y., Tougou, K. and Shinoda, S. Purification and characterization of L-2,4-diaminobutyrate decarboxylase from Acinetobacter calcoaceticus. J. Gen. Microbiol. 138 (1992) 1461–1465. [PMID: 1512577]
2.  Ikai, H. and Yamamoto, S. Cloning and expression in Escherichia coli of the gene encoding a novel L-2,4-diaminobutyrate decarboxylase of Acinetobacter baumannii. FEMS Microbiol. Lett. 124 (1994) 225–228. [PMID: 7813892]
3.  Ikai, H. and Yamamoto, S. Identification and analysis of a gene encoding L-2,4-diaminobutyrate:2-ketoglutarate 4-aminotransferase involved in the 1,3-diaminopropane production pathway in Acinetobacter baumannii. J. Bacteriol. 179 (1997) 5118–5125. [PMID: 9260954]
[EC 4.1.1.86 created 2006]
 
 
EC 4.1.1.87     
Accepted name: malonyl-S-ACP decarboxylase
Reaction: a malonyl-[acyl-carrier protein] + H+ = an acetyl-[acyl-carrier protein] + CO2
Other name(s): malonyl-S-acyl-carrier protein decarboxylase; MdcD/MdcE; MdcD,E
Systematic name: malonyl-[acyl-carrier-protein] carboxy-lyase
Comments: This enzyme comprises the β and γ subunits of EC 4.1.1.88, biotin-independent malonate decarboxylase but is not present in EC 7.2.4.4, biotin-dependent malonate decarboxylase. It follows on from EC 2.3.1.187, acetyl-S-ACP:malonate ACP transferase, and results in the regeneration of the acetylated form of the acyl-carrier-protein subunit of malonate decarboxylase [5]. The carboxy group is lost with retention of configuration [3].
References:
1.  Schmid, M., Berg, M., Hilbi, H. and Dimroth, P. Malonate decarboxylase of Klebsiella pneumoniae catalyses the turnover of acetyl and malonyl thioester residues on a coenzyme-A-like prosthetic group. Eur. J. Biochem. 237 (1996) 221–228. [PMID: 8620876]
2.  Koo, J.H. and Kim, Y.S. Functional evaluation of the genes involved in malonate decarboxylation by Acinetobacter calcoaceticus. Eur. J. Biochem. 266 (1999) 683–690. [PMID: 10561613]
3.  Handa, S., Koo, J.H., Kim, Y.S. and Floss, H.G. Stereochemical course of biotin-independent malonate decarboxylase catalysis. Arch. Biochem. Biophys. 370 (1999) 93–96. [PMID: 10496981]
4.  Chohnan, S., Akagi, K. and Takamura, Y. Functions of malonate decarboxylase subunits from Pseudomonas putida. Biosci. Biotechnol. Biochem. 67 (2003) 214–217. [PMID: 12619701]
5.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [PMID: 11902724]
[EC 4.1.1.87 created 2008]
 
 
EC 4.1.1.88     
Accepted name: biotin-independent malonate decarboxylase
Reaction: malonate + H+ = acetate + CO2
Other name(s): malonate decarboxylase (without biotin); malonate decarboxylase (ambiguous); MDC
Systematic name: malonate carboxy-lyase (biotin-independent)
Comments: Two types of malonate decarboxylase are currently known, both of which form multienzyme complexes. This enzyme is a cytosolic protein that is biotin-independent. The other type is a biotin-dependent, Na+-translocating enzyme that includes both soluble and membrane-bound components (cf. EC 7.2.4.4, biotin-dependent malonate decarboxylase). As free malonate is chemically rather inert, it has to be activated prior to decarboxylation. In both enzymes, this is achieved by exchanging malonate with an acetyl group bound to an acyl-carrier protiein (ACP), to form malonyl-ACP and acetate, with subsequent decarboxylation regenerating the acetyl-ACP. The ACP subunit of both enzymes differs from that found in fatty-acid biosynthesis by having phosphopantethine attached to a serine side-chain as 2-(5-triphosphoribosyl)-3-dephospho-CoA rather than as phosphopantetheine 4′-phosphate. The individual enzymes involved in carrying out the reaction of this enzyme complex are EC 2.3.1.187 (acetyl-S-ACP:malonate ACP transferase), EC 2.3.1.39 ([acyl-carrier-protein] S-malonyltransferase) and EC 4.1.1.87 (malonyl-S-ACP decarboxylase). The carboxy group is lost with retention of configuration [6].
References:
1.  Schmid, M., Berg, M., Hilbi, H. and Dimroth, P. Malonate decarboxylase of Klebsiella pneumoniae catalyses the turnover of acetyl and malonyl thioester residues on a coenzyme-A-like prosthetic group. Eur. J. Biochem. 237 (1996) 221–228. [PMID: 8620876]
2.  Byun, H.S. and Kim, Y.S. Subunit organization of bacterial malonate decarboxylases: the smallest δ subunit as an acyl-carrier protein. J. Biochem. Mol. Biol. 30 (1997) 132–137.
3.  Hoenke, S., Schmid, M. and Dimroth, P. Sequence of a gene cluster from Klebsiella pneumoniae encoding malonate decarboxylase and expression of the enzyme in Escherichia coli. Eur. J. Biochem. 246 (1997) 530–538. [PMID: 9208947]
4.  Chohnan, S., Fujio, T., Takaki, T., Yonekura, M., Nishihara, H. and Takamura, Y. Malonate decarboxylase of Pseudomonas putida is composed of five subunits. FEMS Microbiol. Lett. 169 (1998) 37–43. [PMID: 9851033]
5.  Hoenke, S., Schmid, M. and Dimroth, P. Identification of the active site of phosphoribosyl-dephospho-coenzyme A transferase and relationship of the enzyme to an ancient class of nucleotidyltransferases. Biochemistry 39 (2000) 13233–13240. [PMID: 11052676]
6.  Handa, S., Koo, J.H., Kim, Y.S. and Floss, H.G. Stereochemical course of biotin-independent malonate decarboxylase catalysis. Arch. Biochem. Biophys. 370 (1999) 93–96. [PMID: 10496981]
7.  Koo, J.H. and Kim, Y.S. Functional evaluation of the genes involved in malonate decarboxylation by Acinetobacter calcoaceticus. Eur. J. Biochem. 266 (1999) 683–690. [PMID: 10561613]
8.  Kim, Y.S. Malonate metabolism: biochemistry, molecular biology, physiology, and industrial application. J. Biochem. Mol. Biol. 35 (2002) 443–451. [PMID: 12359084]
9.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [PMID: 11902724]
[EC 4.1.1.88 created 2008, modified 2018]
 
 
EC 4.1.1.89      
Transferred entry: biotin-dependent malonate decarboxylase. Now EC 7.2.4.4, biotin-dependent malonate decarboxylase
[EC 4.1.1.89 created 2008, deleted 2018]
 
 
EC 4.1.1.90     
Accepted name: peptidyl-glutamate 4-carboxylase
Reaction: peptidyl-4-carboxyglutamate + 2,3-epoxyphylloquinone + H2O = peptidyl-glutamate + CO2 + O2 + phylloquinol
Other name(s): vitamin K-dependent carboxylase; γ-glutamyl carboxylase; peptidyl-glutamate 4-carboxylase (2-methyl-3-phytyl-1,4-naphthoquinone-epoxidizing)
Systematic name: peptidyl-glutamate 4-carboxylase (2-methyl-3-phytyl-1,4-naphthoquinol-epoxidizing)
Comments: The enzyme can use various vitamin-K derivatives, including menaquinol, but does not contain iron. The mechanism appears to involve the generation of a strong base by oxygenation of vitamin K. It catalyses the post-translational carboxylation of glutamate residues of several proteins of the blood-clotting system. 9–12 glutamate residues are converted to 4-carboxyglutamate (Gla) in a specific domain of the target protein. The 4-pro-S hydrogen of the glutamate residue is removed [5] and there is an inversion of stereochemistry at this position [6].
References:
1.  Dowd, P., Hershline, R., Ham, S.W. and Naganathan, S. Vitamin K and energy transduction: a base strength amplification mechanism. Science 269 (1995) 1684–1691. [PMID: 7569894]
2.  Furie, B., Bouchard, B.A. and Furie, B.C. Vitamin K-dependent biosynthesis of γ-carboxyglutamic acid. Blood 93 (1999) 1798–1808. [PMID: 10068650]
3.  Rishavy, M.A., Hallgren, K.W., Yakubenko, A.V., Shtofman, R.L., Runge, K.W. and Berkner, K.L. Bronsted analysis reveals Lys218 as the carboxylase active site base that deprotonates vitamin K hydroquinone to initiate vitamin K-dependent protein carboxylation. Biochemistry 45 (2006) 13239–13248. [PMID: 17073445]
4.  Silva, P.J. and Ramos, M.J. Reaction mechanism of the vitamin K-dependent glutamate carboxylase: a computational study. J. Phys. Chem. B 111 (2007) 12883–12887. [PMID: 17935315]
5.  Decottignies-Le Maréchal, P., Ducrocq, C., Marquet, A. and Azerad, R. The stereochemistry of hydrogen abstraction in vitamin K-dependent carboxylation. J. Biol. Chem. 259 (1984) 15010–15012. [PMID: 6150930]
6.  Dubois, J., Dugave, C., Foures, C., Kaminsky, M., Tabet, J.C., Bory, S., Gaudry, M. and Marquet, A. Vitamin K dependent carboxylation: determination of the stereochemical course using 4-fluoroglutamyl-containing substrate. Biochemistry 30 (1991) 10506–10512. [PMID: 1931973]
7.  Rishavy, M.A. and Berkner, K.L. Vitamin K oxygenation, glutamate carboxylation, and processivity: defining the three critical facets of catalysis by the vitamin K-dependent carboxylase. Adv Nutr 3 (2012) 135–148. [PMID: 22516721]
[EC 4.1.1.90 created 2009, modified 2011]
 
 
EC 4.1.1.91     
Accepted name: salicylate decarboxylase
Reaction: salicylate = phenol + CO2
Other name(s): salicylic acid decarboxylase; Scd
Systematic name: salicylate carboxy-lyase
Comments: In the reverse direction the enzyme catalyses the regioselective carboxylation of phenol into stoichiometric amounts of salicylate. The enzyme also catalyses the reversible decarboxylation of 2,4-dihydroxybenzoate, 2,6-dihydroxybenzoate, 2,3-dihydroxybenzoate and 4-aminosalicylate [1].
References:
1.  Kirimura, K., Gunji, H., Wakayama, R., Hattori, T. and Ishii, Y. Enzymatic Kolbe-Schmitt reaction to form salicylic acid from phenol: enzymatic characterization and gene identification of a novel enzyme, Trichosporon moniliiforme salicylic acid decarboxylase. Biochem. Biophys. Res. Commun. 394 (2010) 279–284. [PMID: 20188702]
[EC 4.1.1.91 created 2011]
 
 
EC 4.1.1.92     
Accepted name: indole-3-carboxylate decarboxylase
Reaction: indole-3-carboxylate = indole + CO2
Systematic name: indole-3-carboxylate carboxy-lyase
Comments: Activated by Zn2+, Mn2+ or Mg2+.
References:
1.  Yoshida, T., Fujita, K. and Nagasawa, T. Novel reversible indole-3-carboxylate decarboxylase catalyzing nonoxidative decarboxylation. Biosci. Biotechnol. Biochem. 66 (2002) 2388–2394. [PMID: 12506977]
[EC 4.1.1.92 created 2011]
 
 
EC 4.1.1.93     
Accepted name: pyrrole-2-carboxylate decarboxylase
Reaction: (1) pyrrole-2-carboxylate = pyrrole + CO2
(2) pyrrole-2-carboxylate + H2O = pyrrole + HCO3-
Systematic name: pyrrole-2-carboxylate carboxy-lyase
Comments: The enzyme catalyses both the carboxylation and decarboxylation reactions. However, while bicarbonate is the preferred substrate for the carboxylation reaction, decarboxylation produces carbon dioxide. The enzyme is activated by carboxylic acids.
References:
1.  Wieser, M., Fujii, N., Yoshida, T. and Nagasawa, T. Carbon dioxide fixation by reversible pyrrole-2-carboxylate decarboxylase from Bacillus megaterium PYR2910. Eur. J. Biochem. 257 (1998) 495–499. [PMID: 9826198]
2.  Omura, H., Wieser, M. and Nagasawa, T. Pyrrole-2-carboxylate decarboxylase from Bacillus megaterium PYR2910, an organic-acid-requiring enzyme. Eur. J. Biochem. 253 (1998) 480–484. [PMID: 9654100]
3.  Wieser, M., Yoshida, T. and Nagasawa, T. Microbial synthesis of pyrrole-2-carboxylate by Bacillus megaterium PYR2910. Tetrahedron Lett. 39 (1998) 4309–4310.
[EC 4.1.1.93 created 2011]
 
 
EC 4.1.1.94     
Accepted name: ethylmalonyl-CoA decarboxylase
Reaction: (S)-ethylmalonyl-CoA = butanoyl-CoA + CO2
Systematic name: (S)-ethylmalonyl-CoA carboxy-lyase (butanoyl-CoA-forming)
Comments: The enzyme, which exists in all vertebrates, decarboxylates ethylmalonyl-CoA, a potentially toxic compound that is formed in low amounts by the activity of EC 6.4.1.2, acetyl-CoA carboxylase and EC 6.4.1.3, propanoyl-CoA carboxylase. It prefers the S isomer, and can decarboxylate (R)-ethylmalonyl-CoA with lower efficiency. cf. EC 7.2.4.1, (S)-methylmalonyl-CoA decarboxylase (sodium-transporting).
References:
1.  Linster, C.L., Noel, G., Stroobant, V., Vertommen, D., Vincent, M.F., Bommer, G.T., Veiga-da-Cunha, M. and Van Schaftingen, E. Ethylmalonyl-CoA decarboxylase, a new enzyme involved in metabolite proofreading. J. Biol. Chem. 286 (2011) 42992–43003. [PMID: 22016388]
[EC 4.1.1.94 created 2012]
 
 
EC 4.1.1.95     
Accepted name: L-glutamyl-[BtrI acyl-carrier protein] decarboxylase
Reaction: L-glutamyl-[BtrI acyl-carrier protein] = 4-amino butanoyl-[BtrI acyl-carrier protein] + CO2
Other name(s): btrK (gene name)
Systematic name: L-glutamyl-[BtrI acyl-carrier protein] carboxy-lyase
Comments: Binds pyridoxal 5′-phosphate. Catalyses a step in the biosynthesis of the side chain of the aminoglycoside antibiotics of the butirosin family. Has very low activity with substrates not bound to an acyl-carrier protein.
References:
1.  Li, Y., Llewellyn, N.M., Giri, R., Huang, F. and Spencer, J.B. Biosynthesis of the unique amino acid side chain of butirosin: possible protective-group chemistry in an acyl carrier protein-mediated pathway. Chem. Biol. 12 (2005) 665–675. [PMID: 15975512]
[EC 4.1.1.95 created 2012]
 
 
EC 4.1.1.96     
Accepted name: carboxynorspermidine decarboxylase
Reaction: (1) carboxynorspermidine = bis(3-aminopropyl)amine + CO2
(2) carboxyspermidine = spermidine + CO2
Glossary: bis(3-aminopropyl)amine = norspermidine
Other name(s): carboxyspermidine decarboxylase; CANSDC; VC1623 (gene name)
Systematic name: carboxynorspermidine carboxy-lyase (bis(3-aminopropyl)amine-forming)
Comments: A pyridoxal 5′-phosphate enzyme. Part of a bacterial polyamine biosynthesis pathway. The enzyme is essential for biofilm formation in the bacterium Vibrio cholerae [1]. The enzyme from Campylobacter jejuni only produces spermidine in vivo even though it shows activity with carboxynorspermidine in vitro [3].
References:
1.  Lee, J., Sperandio, V., Frantz, D.E., Longgood, J., Camilli, A., Phillips, M.A. and Michael, A.J. An alternative polyamine biosynthetic pathway is widespread in bacteria and essential for biofilm formation in Vibrio cholerae. J. Biol. Chem. 284 (2009) 9899–9907. [PMID: 19196710]
2.  Deng, X., Lee, J., Michael, A.J., Tomchick, D.R., Goldsmith, E.J. and Phillips, M.A. Evolution of substrate specificity within a diverse family of β/α-barrel-fold basic amino acid decarboxylases: X-ray structure determination of enzymes with specificity for L-arginine and carboxynorspermidine. J. Biol. Chem. 285 (2010) 25708–25719. [PMID: 20534592]
3.  Hanfrey, C.C., Pearson, B.M., Hazeldine, S., Lee, J., Gaskin, D.J., Woster, P.M., Phillips, M.A. and Michael, A.J. Alternative spermidine biosynthetic route is critical for growth of Campylobacter jejuni and is the dominant polyamine pathway in human gut microbiota. J. Biol. Chem. 286 (2011) 43301–43312. [PMID: 22025614]
[EC 4.1.1.96 created 2012]
 
 
EC 4.1.1.97     
Accepted name: 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase
Reaction: 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate = (S)-allantoin + CO2
Glossary: 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate = 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline
Other name(s): OHCU decarboxylase; hpxQ (gene name); PRHOXNB (gene name)
Systematic name: 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate carboxy-lyase [(S)-allantoin-forming]
Comments: This enzyme is part of the pathway from urate to (S)-allantoin, which is present in bacteria, plants and animals (but not in humans).
References:
1.  Ramazzina, I., Folli, C., Secchi, A., Berni, R. and Percudani, R. Completing the uric acid degradation pathway through phylogenetic comparison of whole genomes. Nat. Chem. Biol. 2 (2006) 144–148. [PMID: 16462750]
2.  Cendron, L., Berni, R., Folli, C., Ramazzina, I., Percudani, R. and Zanotti, G. The structure of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase provides insights into the mechanism of uric acid degradation. J. Biol. Chem. 282 (2007) 18182–18189. [PMID: 17428786]
3.  Kim, K., Park, J. and Rhee, S. Structural and functional basis for (S)-allantoin formation in the ureide pathway. J. Biol. Chem. 282 (2007) 23457–23464. [PMID: 17567580]
4.  French, J.B. and Ealick, S.E. Structural and mechanistic studies on Klebsiella pneumoniae 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase. J. Biol. Chem. 285 (2010) 35446–35454. [PMID: 20826786]
[EC 4.1.1.97 created 2014]
 
 
EC 4.1.1.98     
Accepted name: 4-hydroxy-3-polyprenylbenzoate decarboxylase
Reaction: a 4-hydroxy-3-polyprenylbenzoate = a 2-polyprenylphenol + CO2
Other name(s): ubiD (gene name); 4-hydroxy-3-solanesylbenzoate decarboxylase; 3-octaprenyl-4-hydroxybenzoate decarboxylase
Systematic name: 4-hydroxy-3-polyprenylbenzoate carboxy-lyase
Comments: The enzyme catalyses a step in prokaryotic ubiquinone biosynthesis, as well as in plastoquinone biosynthesis in cyanobacteria. The enzyme can accept substrates with different polyprenyl tail lengths in vitro, but uses a specific length in vivo, which is determined by the polyprenyl diphosphate synthase that exists in the specific organism. It requires a prenylated flavin cofactor that is produced by EC 2.5.1.129, flavin prenyltransferase.
References:
1.  Leppik, R.A., Young, I.G. and Gibson, F. Membrane-associated reactions in ubiquinone biosynthesis in Escherichia coli. 3-Octaprenyl-4-hydroxybenzoate carboxy-lyase. Biochim. Biophys. Acta 436 (1976) 800–810. [PMID: 782527]
2.  Gulmezian, M., Hyman, K.R., Marbois, B.N., Clarke, C.F. and Javor, G.T. The role of UbiX in Escherichia coli coenzyme Q biosynthesis. Arch. Biochem. Biophys. 467 (2007) 144–153. [PMID: 17889824]
3.  Pfaff, C., Glindemann, N., Gruber, J., Frentzen, M. and Sadre, R. Chorismate pyruvate-lyase and 4-hydroxy-3-solanesylbenzoate decarboxylase are required for plastoquinone biosynthesis in the cyanobacterium Synechocystis sp. PCC6803. J. Biol. Chem. 289 (2014) 2675–2686. [PMID: 24337576]
4.  Lin, F., Ferguson, K.L., Boyer, D.R., Lin, X.N. and Marsh, E.N. Isofunctional enzymes PAD1 and UbiX catalyze formation of a novel cofactor required by ferulic acid decarboxylase and 4-hydroxy-3-polyprenylbenzoic acid decarboxylase. ACS Chem. Biol. 10 (2015) 1137–1144. [PMID: 25647642]
5.  Payne, K.A., White, M.D., Fisher, K., Khara, B., Bailey, S.S., Parker, D., Rattray, N.J., Trivedi, D.K., Goodacre, R., Beveridge, R., Barran, P., Rigby, S.E., Scrutton, N.S., Hay, S. and Leys, D. New cofactor supports α,β-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition. Nature 522 (2015) 497–501. [PMID: 26083754]
[EC 4.1.1.98 created 2014, modified 2015]
 
 
EC 4.1.1.99     
Accepted name: phosphomevalonate decarboxylase
Reaction: ATP + (R)-5-phosphomevalonate = ADP + phosphate + isopentenyl phosphate + CO2
Systematic name: ATP:(R)-5-phosphomevalonate carboxy-lyase (adding ATP; isopentenyl-phosphate-forming)
Comments: The enzyme participates in a mevalonate pathway that occurs in halophilic archaea. The activity is also present in eubacteria of the Chloroflexi phylum. cf. EC 4.1.1.33, diphosphomevalonate decarboxylase, and EC 4.1.1.110, bisphosphomevalonate decarboxylase.
References:
1.  Dellas, N., Thomas, S.T., Manning, G. and Noel, J.P. Discovery of a metabolic alternative to the classical mevalonate pathway. Elife 2:e00672 (2013). [PMID: 24327557]
2.  Vannice, J.C., Skaff, D.A., Keightley, A., Addo, J.K., Wyckoff, G.J. and Miziorko, H.M. Identification in Haloferax volcanii of phosphomevalonate decarboxylase and isopentenyl phosphate kinase as catalysts of the terminal enzyme reactions in an archaeal alternate mevalonate pathway. J. Bacteriol. 196 (2014) 1055–1063. [PMID: 24375100]
3.  Thomas, S.T., Louie, G.V., Lubin, J.W., Lundblad, V. and Noel, J.P. Substrate Specificity and Engineering of Mevalonate 5-Phosphate Decarboxylase. ACS Chem. Biol. 14 (2019) 1767–1779. [PMID: 31268677]
[EC 4.1.1.99 created 2014, modified 2018]
 
 
EC 4.1.1.100     
Accepted name: prephenate decarboxylase
Reaction: prephenate = 3-[(4R)-4-hydroxycyclohexa-1,5-dien-1-yl]-2-oxopropanoate + CO2
Glossary: L-anticapsin = 3-[(1R,2S,6R)-5-oxo-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine
Other name(s): BacA; AerD; SalX; non-aromatizing prephenate decarboxylase
Systematic name: prephenate carboxy-lyase (3-[(4R)-4-hydroxycyclohexa-1,5-dien-1-yl]-2-oxopropanoate-forming)
Comments: The enzyme, characterized from the bacterium Bacillus subtilis, is involved in the biosynthesis of the nonribosomally synthesized dipeptide antibiotic bacilysin, composed of L-alanine and L-anticapsin. The enzyme isomerizes only the pro-R double bond in prephenate.
References:
1.  Mahlstedt, S.A. and Walsh, C.T. Investigation of anticapsin biosynthesis reveals a four-enzyme pathway to tetrahydrotyrosine in Bacillus subtilis. Biochemistry 49 (2010) 912–923. [PMID: 20052993]
2.  Mahlstedt, S., Fielding, E.N., Moore, B.S. and Walsh, C.T. Prephenate decarboxylases: a new prephenate-utilizing enzyme family that performs nonaromatizing decarboxylation en route to diverse secondary metabolites. Biochemistry 49 (2010) 9021–9023. [PMID: 20863139]
3.  Parker, J.B. and Walsh, C.T. Olefin isomerization regiochemistries during tandem action of BacA and BacB on prephenate in bacilysin biosynthesis. Biochemistry 51 (2012) 3241–3251. [PMID: 22483065]
[EC 4.1.1.100 created 2015]
 
 
EC 4.1.1.101     
Accepted name: malolactic enzyme
Reaction: (S)-malate = (S)-lactate + CO2
Other name(s): mleA (gene name); mleS (gene name)
Systematic name: (S)-malate carboxy-lyase
Comments: The enzyme is involved in the malolactic fermentation of wine, which results in a natural decrease in acidity and favorable changes in wine flavors. It has been purified from several lactic acid bacteria, including Leuconostoc mesenteroides [1], Lactobacillus plantarum [2], and Oenococcus oeni [3,4]. The enzyme contains a tightly bound NAD+ cofactor and requires Mn2+.
References:
1.  Lonvaud-Funel, A. and de Saad, A.M. Purification and properties of a malolactic Enzyme from a strain of Leuconostoc mesenteroides isolated from grapes. Appl. Environ. Microbiol. 43 (1982) 357–361. [PMID: 16345941]
2.  Caspritz, G. and Radler, F. Malolactic enzyme of Lactobacillus plantarum. Purification, properties, and distribution among bacteria. J. Biol. Chem. 258 (1983) 4907–4910. [PMID: 6833282]
3.  Naouri, P., Chagnaud, P., Arnaud, A. and Galzy, P. Purification and properties of a malolactic enzyme from Leuconostoc oenos ATCC 23278. J. Basic Microbiol. 30 (1990) 577–585. [PMID: 2097345]
4.  Schumann, C., Michlmayr, H., Del Hierro, A.M., Kulbe, K.D., Jiranek, V., Eder, R. and Nguyen, T.H. Malolactic enzyme from Oenococcus oeni: heterologous expression in Escherichia coli and biochemical characterization. Bioengineered 4 (2013) 147–152. [PMID: 23196745]
[EC 4.1.1.101 created 2015]
 
 
EC 4.1.1.102     
Accepted name: phenacrylate decarboxylase
Reaction: (1) 4-coumarate = 4-vinylphenol + CO2
(2) trans-cinnamate = styrene + CO2
(3) ferulate = 4-vinylguaiacol + CO2
Glossary: 4-coumarate = 3-(4-hydroxyphenyl)prop-2-enoate
trans-cinnamate = (2E)-3-phenylprop-2-enoate
ferulate = 4-hydroxy-3-methoxycinnamate
Other name(s): FDC1 (gene name); ferulic acid decarboxylase
Systematic name: 3-phenylprop-2-enoate carboxy-lyase
Comments: The enzyme, found in fungi, catalyses the decarboxylation of phenacrylic acids present in plant cell walls. It requires a prenylated flavin cofactor that is produced by EC 2.5.1.129, flavin prenyltransferase.
References:
1.  Mukai, N., Masaki, K., Fujii, T., Kawamukai, M. and Iefuji, H. PAD1 and FDC1 are essential for the decarboxylation of phenylacrylic acids in Saccharomyces cerevisiae. J. Biosci. Bioeng. 109 (2010) 564–569. [PMID: 20471595]
2.  Bhuiya, M.W., Lee, S.G., Jez, J.M. and Yu, O. Structure and mechanism of ferulic acid decarboxylase (FDC1) from Saccharomyces cerevisiae. Appl. Environ. Microbiol. 81 (2015) 4216–4223. [PMID: 25862228]
3.  Payne, K.A., White, M.D., Fisher, K., Khara, B., Bailey, S.S., Parker, D., Rattray, N.J., Trivedi, D.K., Goodacre, R., Beveridge, R., Barran, P., Rigby, S.E., Scrutton, N.S., Hay, S. and Leys, D. New cofactor supports α,β-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition. Nature 522 (2015) 497–501. [PMID: 26083754]
[EC 4.1.1.102 created 2015]
 
 
EC 4.1.1.103     
Accepted name: γ-resorcylate decarboxylase
Reaction: 2,6-dihydroxybenzoate = 1,3-dihydroxybenzene + CO2
Glossary: 2,6-dihydroxybenzoate = γ-resorcylate
1,3-dihydroxybenzene = resorcinol
Other name(s): graF (gene name); tsdA (gene name)
Systematic name: 2,6-dihydroxybenzoate carboxy-lyase
Comments: The enzyme, characterized from several bacterial strains, is involved in the degradation of γ-resorcylate. It contains a zinc ion and a water molecule at the active site. The reaction is reversible, but equilibrium greatly favors the decarboxylation reaction.
References:
1.  Yoshida, M., Fukuhara, N. and Oikawa, T. Thermophilic, reversible γ-resorcylate decarboxylase from Rhizobium sp. strain MTP-10005: purification, molecular characterization, and expression. J. Bacteriol. 186 (2004) 6855–6863. [PMID: 15466039]
2.  Ishii, Y., Narimatsu, Y., Iwasaki, Y., Arai, N., Kino, K. and Kirimura, K. Reversible and nonoxidative γ-resorcylic acid decarboxylase: characterization and gene cloning of a novel enzyme catalyzing carboxylation of resorcinol, 1,3-dihydroxybenzene, from Rhizobium radiobacter. Biochem. Biophys. Res. Commun. 324 (2004) 611–620. [PMID: 15474471]
3.  Matsui, T., Yoshida, T., Yoshimura, T. and Nagasawa, T. Regioselective carboxylation of 1,3-dihydroxybenzene by 2,6-dihydroxybenzoate decarboxylase of Pandoraea sp. 12B-2. Appl. Microbiol. Biotechnol. 73 (2006) 95–102. [PMID: 16683134]
4.  Goto, M., Hayashi, H., Miyahara, I., Hirotsu, K., Yoshida, M. and Oikawa, T. Crystal structures of nonoxidative zinc-dependent 2,6-dihydroxybenzoate (γ-resorcylate) decarboxylase from Rhizobium sp. strain MTP-10005. J. Biol. Chem. 281 (2006) 34365–34373. [PMID: 16963440]
5.  Kasai, D., Araki, N., Motoi, K., Yoshikawa, S., Iino, T., Imai, S., Masai, E. and Fukuda, M. γ-Resorcylate catabolic-pathway genes in the soil actinomycete Rhodococcus jostii RHA1. Appl. Environ. Microbiol. 81 (2015) 7656–7665. [PMID: 26319878]
[EC 4.1.1.103 created 2016]
 
 
EC 4.1.1.104     
Accepted name: 3-dehydro-4-phosphotetronate decarboxylase
Reaction: (1) 3-dehydro-4-phospho-L-erythronate = glycerone phosphate + CO2
(2) 3-dehydro-4-phospho-D-erythronate = glycerone phosphate + CO2
Glossary: L-erythronate = (2S,3S)-2,3,4-trihydroxybutanoate
D-erythronate = (2R,3R)-2,3,4-trihydroxybutanoate
Other name(s): otnC (gene name)
Systematic name: 3-dehydro-4-phosphotetronate carboxy-lyase
Comments: The enzyme, characterized from bacteria, is involved in D-erythronate and L-threonate catabolism.
References:
1.  Zhang, X., Carter, M.S., Vetting, M.W., San Francisco, B., Zhao, S., Al-Obaidi, N.F., Solbiati, J.O., Thiaville, J.J., de Crecy-Lagard, V., Jacobson, M.P., Almo, S.C. and Gerlt, J.A. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc. Natl. Acad. Sci. USA 113 (2016) E4161–E4169. [PMID: 27402745]
[EC 4.1.1.104 created 2017]
 
 
EC 4.1.1.105     
Accepted name: L-tryptophan decarboxylase
Reaction: L-tryptophan = tryptamine + CO2
Other name(s): psiD (gene name); TDC (gene name)
Systematic name: L-tryptophan carboxy-lyase
Comments: The enzyme has been characterized from bacteria, plants, and fungi. Unlike EC 4.1.1.28, aromatic-L-amino-acid decarboxylase, this enzyme is specific for L-tryptophan.
References:
1.  Noe, W., Mollenschott, C. and Berlin, J. Tryptophan decarboxylase from Catharanthus roseus cell suspension cultures: purification, molecular and kinetic data of the homogenous protein. Plant Mol. Biol. 3 (1984) 281–288. [PMID: 24310513]
2.  Buki, K.G., Vinh, D.Q. and Horvath, I. Partial purification and some properties of tryptophan decarboxylase from a Bacillus strain. Acta Microbiol Hung 32 (1985) 65–73. [PMID: 4036551]
3.  Nakazawa, H., Kumagai, H. and Yamada, H. Constitutive aromatic L-amino acid decarboxylase from Micrococcus percitreus. Biochem. Biophys. Res. Commun. 61 (1974) 75–82. [PMID: 4441405]
4.  Lopez-Meyer, M. and Nessler, C.L. Tryptophan decarboxylase is encoded by two autonomously regulated genes in Camptotheca acuminata which are differentially expressed during development and stress. Plant J. 11 (1997) 1167–1175. [PMID: 9225462]
5.  Fricke, J., Blei, F. and Hoffmeister, D. Enzymatic synthesis of psilocybin. Angew. Chem. Int. Ed. Engl. 56 (2017) 12352–12355. [PMID: 28763571]
[EC 4.1.1.105 created 2017]
 
 
EC 4.1.1.106     
Accepted name: fatty acid photodecarboxylase
Reaction: a long-chain fatty acid + = a long-chain alkane + CO2
Other name(s): FAP (gene name)
Systematic name: fatty acid carboxy-lyase (light-dependent, alkane-forming)
Comments: This algal enzyme, characterized from the green algae Chlorella variabilis and Chlamydomonas reinhardtii, is dependent on blue light, which photooxidizes its FAD cofactor. The enzyme acts on fatty acids in the range of C12 to C22, with a higher efficiency for C16 to C17 chains, and forms an alkane product that is one carbon shorter than the substrate. The enzyme can also act on unsaturated fatty acids, forming the respective alkenes, but does not generate a new double bond.
References:
1.  Sorigue, D., Legeret, B., Cuine, S., Blangy, S., Moulin, S., Billon, E., Richaud, P., Brugiere, S., Coute, Y., Nurizzo, D., Muller, P., Brettel, K., Pignol, D., Arnoux, P., Li-Beisson, Y., Peltier, G. and Beisson, F. An algal photoenzyme converts fatty acids to hydrocarbons. Science 357 (2017) 903–907. [PMID: 28860382]
[EC 4.1.1.106 created 2017]
 
 
EC 4.1.1.107     
Accepted name: 3,4-dihydroxyphenylacetaldehyde synthase
Reaction: L-dopa + O2 + H2O = 3,4-dihydroxyphenylacetaldehyde + CO2 + NH3 + H2O2
Glossary: L-dopa = 3,4-dihydroxyphenylalanine
Other name(s): DHPAA synthase
Systematic name: L-dopa carboxy-lyase (oxidative-deaminating)
Comments: A pyridoxal 5′-phosphate protein. The enzyme, isolated from the mosquito Aedes aegypti, catalyses the production of 3,4-dihydroxylphenylacetaldehyde directly from L-dopa. Dopamine is not formed as an intermediate (cf. EC 4.1.1.28, aromatic-L-amino-acid decarboxylase). The enzyme is specific for L-dopa and does not react with other aromatic amino acids with the exception of a low activity with α-methyl-L-dopa.
References:
1.  Vavricka, C., Han, Q., Huang, Y., Erickson, S.M., Harich, K., Christensen, B.M. and Li, J. From L-dopa to dihydroxyphenylacetaldehyde: a toxic biochemical pathway plays a vital physiological function in insects. PLoS One 6:e16124 (2011). [PMID: 21283636]
[EC 4.1.1.107 created 2017]
 
 
EC 4.1.1.108     
Accepted name: 4-hydroxyphenylacetaldehyde synthase
Reaction: L-tyrosine + O2 + H2O = (4-hydroxyphenyl)acetaldehyde + CO2 + NH3 + H2O2
Other name(s): TYRDC-2 (gene name)
Systematic name: L-tyrosine carboxy-lyase (oxidative-deaminating)
Comments: A pyridoxal 5′-phosphate protein. The enzyme, isolated from the the plant Petroselinum crispum (parsley), catalyses the production of 4-hydroxyphenylacetaldehyde directly from L-tyrosine. Tyramine is not formed as an intermediate. The enzyme has a low activity with L-dopa (cf. EC 4.1.1.107, 3,4-dihydroxyphenylacetaldehyde synthase).
References:
1.  Torrens-Spence, M.P., Gillaspy, G., Zhao, B., Harich, K., White, R.H. and Li, J. Biochemical evaluation of a parsley tyrosine decarboxylase results in a novel 4-hydroxyphenylacetaldehyde synthase enzyme. Biochem. Biophys. Res. Commun. 418 (2012) 211–216. [PMID: 22266321]
2.  Torrens-Spence, M.P., Liu, P., Ding, H., Harich, K., Gillaspy, G. and Li, J. Biochemical evaluation of the decarboxylation and decarboxylation-deamination activities of plant aromatic amino acid decarboxylases. J. Biol. Chem. 288 (2013) 2376–2387. [PMID: 23204519]
[EC 4.1.1.108 created 2017]
 
 
EC 4.1.1.109     
Accepted name: phenylacetaldehyde synthase
Reaction: L-phenylalanine + O2 + H2O = phenylacetaldehyde + CO2 + NH3 + H2O2
Other name(s): PAAS (gene name)
Systematic name: L-phenylalanine carboxy-lyase (oxidative-deaminating)
Comments: A pyridoxal 5′-phosphate protein. The enzyme, isolated from the the plants Petunia hybrida and a Rosa hybrid, catalyses the production of phenylacetaldehyde directly from L-phenylalanine. The enzyme is specific for L-phenylalanine and does not accept other aromatic amino acids as substrates.
References:
1.  Kaminaga, Y., Schnepp, J., Peel, G., Kish, C.M., Ben-Nissan, G., Weiss, D., Orlova, I., Lavie, O., Rhodes, D., Wood, K., Porterfield, D.M., Cooper, A.J., Schloss, J.V., Pichersky, E., Vainstein, A. and Dudareva, N. Plant phenylacetaldehyde synthase is a bifunctional homotetrameric enzyme that catalyzes phenylalanine decarboxylation and oxidation. J. Biol. Chem. 281 (2006) 23357–23366. [PMID: 16766535]
[EC 4.1.1.109 created 2017]
 
 
EC 4.1.1.110     
Accepted name: bisphosphomevalonate decarboxylase
Reaction: (R)-3,5-bisphosphomevalonate = isopentenyl phosphate + CO2 + phosphate
Other name(s): mevalonate 3,5-bisphosphate decarboxylase
Systematic name: (R)-3,5-bisphosphomevalonate carboxy-lyase (isopentenyl-phosphate-forming)
Comments: The enzyme participates in an alternative mevalonate pathway that takes place in extreme acidophiles of the Thermoplasmatales order. cf. EC 4.1.1.99, phosphomevalonate decarboxylase.
References:
1.  Vinokur, J.M., Cummins, M.C., Korman, T.P. and Bowie, J.U. An adaptation to life in acid through a novel mevalonate pathway. Sci. Rep. 6 (2016) 39737. [PMID: 28004831]
[EC 4.1.1.110 created 2018]
 
 
EC 4.1.1.111     
Accepted name: siroheme decarboxylase
Reaction: siroheme = 12,18-didecarboxysiroheme + 2 CO2
Other name(s): sirohaem decarboxylase; nirDLHG (gene name); ahbAB (gene name)
Systematic name: siroheme carboxy-lyase
Comments: The enzyme from archaea is involved in an alternative heme biosynthesis pathway. The enzyme from denitrifying bacteria is involved in the heme d1 biosynthesis pathway.
References:
1.  Bali, S., Lawrence, A.D., Lobo, S.A., Saraiva, L.M., Golding, B.T., Palmer, D.J., Howard, M.J., Ferguson, S.J. and Warren, M.J. Molecular hijacking of siroheme for the synthesis of heme and d1 heme. Proc. Natl. Acad. Sci. USA 108 (2011) 18260–18265. [PMID: 21969545]
2.  Kuhner, M., Haufschildt, K., Neumann, A., Storbeck, S., Streif, J. and Layer, G. The alternative route to heme in the methanogenic archaeon Methanosarcina barkeri. Archaea 2014:327637 (2014). [PMID: 24669201]
3.  Palmer, D.J., Schroeder, S., Lawrence, A.D., Deery, E., Lobo, S.A., Saraiva, L.M., McLean, K.J., Munro, A.W., Ferguson, S.J., Pickersgill, R.W., Brown, D.G. and Warren, M.J. The structure, function and properties of sirohaem decarboxylase--an enzyme with structural homology to a transcription factor family that is part of the alternative haem biosynthesis pathway. Mol. Microbiol. 93 (2014) 247–261. [PMID: 24865947]
4.  Haufschildt, K., Schmelz, S., Kriegler, T.M., Neumann, A., Streif, J., Arai, H., Heinz, D.W. and Layer, G. The crystal structure of siroheme decarboxylase in complex with iron-uroporphyrin III reveals two essential histidine residues. J. Mol. Biol. 426 (2014) 3272–3286. [PMID: 25083922]
[EC 4.1.1.111 created 2018]
 
 
EC 4.1.1.112     
Accepted name: oxaloacetate decarboxylase
Reaction: oxaloacetate = pyruvate + CO2
Other name(s): oxaloacetate β-decarboxylase; oxalacetic acid decarboxylase; oxalate β-decarboxylase; oxaloacetate carboxy-lyase
Systematic name: oxaloacetate carboxy-lyase (pyruvate-forming)
Comments: Requires a divalent metal cation. The enzymes from the fish Gadus morhua (Atlantic cod) and the bacterium Micrococcus luteus prefer Mn2+, while those from the bacteria Pseudomonas putida and Pseudomonas aeruginosa prefer Mg2+. Unlike EC 7.2.4.2 [oxaloacetate decarboxylase (Na+ extruding)], there is no evidence of the enzyme’s involvement in Na+ transport.
References:
1.  Schmitt, A., Bottke, I. and Siebert, G. Eigenschaften einer Oxaloacetat-Decarboxylase aus Dorschmuskulatur. Hoppe-Seyler's Z. Physiol. Chem. 347 (1966) 18–34. [PMID: 5972993]
2.  Herbert, D. Oxalacetic carboxylase of Micrococcus lysodeikticus. Methods Enzymol. 1 (1955) 753–757.
3.  Horton, A.A. and Kornberg, H.L. Oxaloacetate 4-carboxy-lyase from Pseudomonas ovalis chester. Biochim. Biophys. Acta 89 (1964) 381–383. [PMID: 14205502]
4.  Sender, P.D., Martin, M.G., Peiru, S. and Magni, C. Characterization of an oxaloacetate decarboxylase that belongs to the malic enzyme family. FEBS Lett. 570 (2004) 217–222. [PMID: 15251467]
5.  Narayanan, B.C., Niu, W., Han, Y., Zou, J., Mariano, P.S., Dunaway-Mariano, D. and Herzberg, O. Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily. Biochemistry 47 (2008) 167–182. [PMID: 18081320]
[EC 4.1.1.112 created 1961 as EC 4.1.1.3, modified 1986, modified 2000, part transferred 2018 to EC 4.1.1.112]
 
 
EC 4.1.1.113     
Accepted name: trans-aconitate decarboxylase
Reaction: trans-aconitate = itaconate + CO2
Glossary: trans-aconitate = (E)-prop-1-ene-1,2,3-tricarboxylate
itaconate = 2-methylenesuccinate
Other name(s): TAD1 (gene name)
Systematic name: trans-aconitate carboxy-lyase (itaconate-forming)
Comments: The enzyme, characterized from the smut fungus Ustilago maydis, is involved in an alternative pathway for the biosynthesis of itaconate. cf. EC 4.1.1.6, cis-aconitate decarboxylase.
References:
1.  Geiser, E., Przybilla, S.K., Friedrich, A., Buckel, W., Wierckx, N., Blank, L.M. and Bolker, M. Ustilago maydis produces itaconic acid via the unusual intermediate trans-aconitate. Microb. Biotechnol. 9 (2016) 116–126. [PMID: 26639528]
[EC 4.1.1.113 created 2018]
 
 
EC 4.1.1.114     
Accepted name: cis-3-alkyl-4-alkyloxetan-2-one decarboxylase
Reaction: a cis-3-alkyl-4-alkyloxetan-2-one = a cis-alkene + CO2
Other name(s): oleB (gene name)
Systematic name: cis-3-alkyl-4-alkyloxetan-2-one carboxy-lyase (cis-alkene-forming)
Comments: The enzyme, found in certain bacterial species, catalyses the last step in a pathway for the production of olefins.
References:
1.  Christenson, J.K., Richman, J.E., Jensen, M.R., Neufeld, J.Y., Wilmot, C.M. and Wackett, L.P. β-Lactone synthetase found in the olefin biosynthesis pathway. Biochemistry 56 (2017) 348–351. [PMID: 28029240]
2.  Christenson, J.K., Jensen, M.R., Goblirsch, B.R., Mohamed, F., Zhang, W., Wilmot, C.M. and Wackett, L.P. Active multienzyme assemblies for long-chain olefinic hydrocarbon biosynthesis. J. Bacteriol. 199 (2017) . [PMID: 28223313]
[EC 4.1.1.114 created 2018]
 
 
EC 4.1.1.115     
Accepted name: indoleacetate decarboxylase
Reaction: (1H-indol-3-yl)acetate = skatole + CO2
Glossary: (1H-indol-3-yl)acetate = indoleacetate
skatole = 3-methyl-1H-indole
Other name(s): IAD
Systematic name: (1H-indol-3-yl)acetate carboxy-lyase (skatole-forming)
Comments: This glycyl radical enzyme has been isolate from a number of bacterial species. Skatole contributes to the characteristic smell of animal faeces.
References:
1.  Liu, D., Wei, Y., Liu, X., Zhou, Y., Jiang, L., Yin, J., Wang, F., Hu, Y., Nanjaraj Urs, A.N., Liu, Y., Ang, E.L., Zhao, S., Zhao, H. and Zhang, Y. Indoleacetate decarboxylase is a glycyl radical enzyme catalysing the formation of malodorant skatole. Nat. Commun. 9:4224 (2018). [PMID: 30310076]
[EC 4.1.1.115 created 2019]
 
 
EC 4.1.1.116     
Accepted name: D-ornithine/D-lysine decarboxylase
Reaction: (1) D-ornithine = putrescine + CO2
(2) D-lysine = cadaverine + CO2
Glossary: cadaverine = pentane-1,5-diamine
putrescine = butane-1,4-diamine
Other name(s): dokD (gene name); DOKDC
Systematic name: D-ornithine/D-lysine carboxy-lyase
Comments: The enzyme, characterized from the bacterium Salmonella typhimurium LT2, is specific for D-ornithine and D-lysine. Requires pyridoxal 5′-phosphate.
References:
1.  Phillips, R.S., Poteh, P., Miller, K.A. and Hoover, T.R. STM2360 encodes a D-ornithine/D-lysine decarboxylase in Salmonella enterica serovar typhimurium. Arch. Biochem. Biophys. 634 (2017) 83–87. [PMID: 29024617]
[EC 4.1.1.116 created 2019]
 
 
EC 4.1.1.117     
Accepted name: 2-[(L-alanin-3-ylcarbamoyl)methyl]-2-hydroxybutanedioate decarboxylase
Reaction: 2-[(L-alanin-3-ylcarbamoyl)methyl]-2-hydroxybutanedioate = 2-[(2-aminoethylcarbamoyl)methyl]-2-hydroxybutanedioate + CO2
Glossary: staphyloferrin B = 5-[(2-{[(3S)-5-{[(2S)-2-amino-2-carboxyethyl]amino}-3-carboxy-3-hydroxy-5-oxopentanoyl]amino}ethyl)amino]-2,5-dioxopentanoate
Other name(s): sbnH (gene name)
Systematic name: 2-[(L-alanin-3-ylcarbamoyl)methyl]-2-hydroxybutanedioate carboxy-lyase (2-[(2-aminoethylcarbamoyl)methyl]-2-hydroxybutanedioate-forming)
Comments: The enzyme, characterized from the bacterium Staphylococcus aureus, participates in the biosynthesis of the siderophore staphyloferrin B.
References:
1.  Cheung, J., Beasley, F.C., Liu, S., Lajoie, G.A. and Heinrichs, D.E. Molecular characterization of staphyloferrin B biosynthesis in Staphylococcus aureus. Mol. Microbiol. 74 (2009) 594–608. [PMID: 19775248]
[EC 4.1.1.117 created 2019]
 
 
EC 4.1.1.118     
Accepted name: isophthalyl-CoA decarboxylase
Reaction: isophthalyl-CoA = benzoyl-CoA + CO2
Other name(s): IPCD
Systematic name: isophthalyl-CoA carboxy-lyase
Comments: The enzyme, characterized from the bacterium Syntrophorhabdus aromaticivorans, participates in an anaerobic isophthalate degradation pathway. The enzyme requires a prenylated flavin mononucleotide cofactor.
References:
1.  Junghare, M., Spiteller, D. and Schink, B. Anaerobic degradation of xenobiotic isophthalate by the fermenting bacterium Syntrophorhabdus aromaticivorans. ISME J. 13 (2019) 1252–1268. [PMID: 30647456]
[EC 4.1.1.118 created 2019]
 
 
EC 4.1.1.119     
Accepted name: phenylacetate decarboxylase
Reaction: phenylacetate = toluene + CO2
Other name(s): phdB (gene name)
Systematic name: phenylacetate carboxy-lyase
Comments: This bacterial enzyme, isolated from anoxic, toluene-producing microbial communities, is a glycyl radical enzyme. It needs to be activated by a dedicated activating enzyme (PhdA). The activase catalyses the reductive cleavage of AdoMet, producing a 5′-deoxyadenosyl radical that leads to the production of the glycyl radical in PhdB.
References:
1.  Zargar, K., Saville, R., Phelan, R.M., Tringe, S.G., Petzold, C.J., Keasling, J.D. and Beller, H.R. In vitro characterization of phenylacetate decarboxylase, a novel enzyme catalyzing toluene biosynthesis in an anaerobic microbial community. Sci. Rep. 6:31362 (2016). [PMID: 27506494]
2.  Beller, H.R., Rodrigues, A.V., Zargar, K., Wu, Y.W., Saini, A.K., Saville, R.M., Pereira, J.H., Adams, P.D., Tringe, S.G., Petzold, C.J. and Keasling, J.D. Discovery of enzymes for toluene synthesis from anoxic microbial communities. Nat. Chem. Biol. 14 (2018) 451–457. [PMID: 29556105]
3.  Rodrigues, A.V., Tantillo, D.J., Mukhopadhyay, A., Keasling, J.D. and Beller, H. Insights into the mechanism of phenylacetate decarboxylase (PhdB), a toluene-producing glycyl radical enzyme. ChemBioChem (2019) . [PMID: 31512343]
[EC 4.1.1.119 created 2019]
 
 
EC 4.1.1.120     
Accepted name: 3-oxoisoapionate decarboxylase
Reaction: 3-oxoisoapionate = L-erythrulose + CO2
Glossary: 3-oxoisoapionate = 2,4-dihydroxy-2-(hydroxymethyl)-3-oxobutanoate
Other name(s): oiaC (gene name)
Systematic name: 3-oxoisoapionate carboxy-lyase
Comments: The enzyme, characterized from several bacterial species, is involved in the degradation of D-apionate. Stereospecificity of 3-oxoisoapionate has not been determined.
References:
1.  Carter, M.S., Zhang, X., Huang, H., Bouvier, J.T., Francisco, B.S., Vetting, M.W., Al-Obaidi, N., Bonanno, J.B., Ghosh, A., Zallot, R.G., Andersen, H.M., Almo, S.C. and Gerlt, J.A. Functional assignment of multiple catabolic pathways for D-apiose. Nat. Chem. Biol. 14 (2018) 696–705. [PMID: 29867142]
[EC 4.1.1.120 created 2020]
 
 
EC 4.1.1.121     
Accepted name: 3-oxoisoapionate-4-phosphate decarboxylase
Reaction: 3-oxoisoapionate 4-phosphate = L-erythrulose 1-phosphate + CO2
Glossary: 3-oxoisoapionate = 2,4-dihydroxy-2-(hydroxymethyl)-3-oxobutanoate
Other name(s): oiaX (gene name)
Systematic name: 3-oxoisoapionate 4-phosphate carboxy-lyase
Comments: The enzyme, characterized from several bacterial species, participates in the degradation of D-apionate. It belongs to the RuBisCO-like-protein (RLP) superfamily. Stereospecificity of 3-oxoisoapionate 4-phosphate has not been determined.
References:
1.  Carter, M.S., Zhang, X., Huang, H., Bouvier, J.T., Francisco, B.S., Vetting, M.W., Al-Obaidi, N., Bonanno, J.B., Ghosh, A., Zallot, R.G., Andersen, H.M., Almo, S.C. and Gerlt, J.A. Functional assignment of multiple catabolic pathways for D-apiose. Nat. Chem. Biol. 14 (2018) 696–705. [PMID: 29867142]
[EC 4.1.1.121 created 2020]
 
 
EC 4.1.2.1      
Deleted entry:  hydroxyoxobutyrate aldolase. Now included with EC 4.1.3.16 4-hydroxy-2-oxoglutarate aldolase
[EC 4.1.2.1 created 1961, deleted 1972]
 
 
EC 4.1.2.2     
Accepted name: ketotetrose-phosphate aldolase
Reaction: erythrulose 1-phosphate = glycerone phosphate + formaldehyde
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): phosphoketotetrose aldolase; erythrulose-1-phosphate synthetase; erythrose-1-phosphate synthase; erythrulose-1-phosphate formaldehyde-lyase
Systematic name: erythrulose-1-phosphate formaldehyde-lyase (glycerone-phosphate-forming)
References:
1.  Charalampous, F.C. and Mueller, G.C. Synthesis of erythrulose phosphate by a soluble enzyme from rat tissue. J. Biol. Chem. 201 (1953) 161–173. [PMID: 13044785]
[EC 4.1.2.2 created 1961]
 
 
EC 4.1.2.3      
Deleted entry:  pentosealdolase
[EC 4.1.2.3 created 1961, deleted 1972]
 
 
EC 4.1.2.4     
Accepted name: deoxyribose-phosphate aldolase
Reaction: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde
Other name(s): phosphodeoxyriboaldolase; deoxyriboaldolase; deoxyribose-5-phosphate aldolase; 2-deoxyribose-5-phosphate aldolase; 2-deoxy-D-ribose-5-phosphate acetaldehyde-lyase
Systematic name: 2-deoxy-D-ribose-5-phosphate acetaldehyde-lyase (D-glyceraldehyde-3-phosphate-forming)
References:
1.  Hoffee, P.A. 2-Deoxyribose-5-phosphate aldolase of Salmonella typhimurium: purification and properties. Arch. Biochem. Biophys. 126 (1968) 795–802. [PMID: 4879701]
2.  Jedziniak, J.A. and Lionetti, F.J. Purification and properties of deoxyriboaldolase from human erythrocytes. Biochim. Biophys. Acta 212 (1970) 478–487. [PMID: 4989681]
3.  Racker, E. Enzymatic synthesis and breakdown of desoxyribose phosphate. J. Biol. Chem. 196 (1952) 347–365. [PMID: 12980976]
4.  Hoffee, P. Rosen, O.M. and Horecker, B.L. The mechanism of action of aldolases. VI. Crystallization of deoxyribose 5-phosphate aldolase and the number of active sites. J. Biol. Chem. 240 (1965) 1512–1516. [PMID: 14285485]
[EC 4.1.2.4 created 1961]
 
 
EC 4.1.2.5     
Accepted name: L-threonine aldolase
Reaction: L-threonine = glycine + acetaldehyde
Other name(s): L-threonine acetaldehyde-lyase
Systematic name: L-threonine acetaldehyde-lyase (glycine-forming)
Comments: A pyridoxal-phosphate protein. This enzyme is specific for L-threonine and can not utilize L-allo-threonine. Different from EC 4.1.2.49, L-allo-threonine aldolase, and EC 4.1.2.48, low-specificity L-threonine aldolase.
References:
1.  Dainty, R.H. Purification and properties of threonine aldolase from Clostridium pasteurianum. Biochem. J. 117 (1970) 585–592. [PMID: 5419751]
2.  Karasek, M.A. and Greenberg, D.M. Studies on the properties of threonine aldolases. J. Biol. Chem. 227 (1957) 191–205. [PMID: 13449064]
[EC 4.1.2.5 created 1961, deleted 1972, reinstated 1976, modified 2011]
 
 
EC 4.1.2.6      
Deleted entry:  allothreonine aldolase. Reaction is due to EC 2.1.2.1, glycine hydroxymethyltransferase
[EC 4.1.2.6 created 1961, deleted 1972]
 
 
EC 4.1.2.7      
Deleted entry:  ketose-1-phosphate aldolase. Now included with EC 4.1.2.13 fructose-bisphosphate aldolase
[EC 4.1.2.7 created 1961, deleted 1972]
 
 
EC 4.1.2.8     
Accepted name: indole-3-glycerol-phosphate lyase
Reaction: (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate = indole + D-glyceraldehyde 3-phosphate
Other name(s): tryptophan synthase α; TSA; indoleglycerolphosphate aldolase; indole glycerol phosphate hydrolase; indole synthase; indole-3-glycerolphosphate D-glyceraldehyde-3-phosphate-lyase; indole-3-glycerol phosphate lyase; IGL; BX1; (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate D-glyceraldehyde-3-phosphate-lyase
Systematic name: (1S,2R)-1-C-(indol-3-yl)glycerol-3-phosphate D-glyceraldehyde-3-phosphate-lyase (indole-forming)
Comments: Forms part of the defence mechanism against insects and microbial pathogens in the grass family, Gramineae, where it catalyses the first committed step in the formation of the cyclic hydroxamic acids 2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one (DIBOA) and 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA) [1]. This enzyme resembles the α-subunit of EC 4.2.1.20, tryptophan synthase [3], for which, (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate is also a substrate, but, unlike tryptophan synthase, its activity is independent of the β-subunit and free indole is released [2].
References:
1.  Yanofsky, C. The enzymatic conversion of anthranilic acid to indole. J. Biol. Chem. 223 (1956) 171–184. [PMID: 13376586]
2.  Frey, M., Chomet, P., Glawischnig, E., Stettner, C., Grün, S., Winklmair, A., Eisenreich, W., Bacher, A., Meeley, R.B., Briggs, S.P., Simcox, K. and Gierl, A. Analysis of a chemical plant defense mechanism in grasses. Science 277 (1997) 696–699. [PMID: 9235894]
3.  Frey, M., Stettner, C., Paré, P.W., Schmelz, E.A., Tumlinson, J.H. and Gierl, A. An herbivore elicitor activates the gene for indole emission in maize. Proc. Natl. Acad. Sci. USA 97 (2000) 14801–14806. [PMID: 11106389]
4.  Melanson, D., Chilton, M.D., Masters-Moore, D. and Chilton, W.S. A deletion in an indole synthase gene is responsible for the DIMBOA-deficient phenotype of bxbx maize. Proc. Natl. Acad. Sci. USA 94 (1997) 13345–13350. [PMID: 9371848]
[EC 4.1.2.8 created 1961, deleted 1972, reinstated 2006]
 
 
EC 4.1.2.9     
Accepted name: phosphoketolase
Reaction: D-xylulose 5-phosphate + phosphate = acetyl phosphate + D-glyceraldehyde 3-phosphate + H2O
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): D-xylulose-5-phosphate D-glyceraldehyde-3-phosphate-lyase (phosphate-acetylating)
Systematic name: D-xylulose-5-phosphate D-glyceraldehyde-3-phosphate-lyase (adding phosphate; acetyl-phosphate-forming)
Comments: A thiamine-diphosphate protein.
References:
1.  Heath, E.C., Hurwitz, J., Horecker, B.L. and Ginsburg, A. Pentose fermentation by Lactobacillus plantarum. I. The cleavage of xylulose 5-phosphate by phosphoketolase. J. Biol. Chem. 231 (1958) 1009–1029. [PMID: 13539033]
2.  Schramm, M., Klybas, V. and Racker, E. Phospholytic cleavage of fructose-6-phosphate by fructose-6-phosphate phosphoketolase from Acetobacter xylinum. J. Biol. Chem. 233 (1958) 1283–1288. [PMID: 13610828]
[EC 4.1.2.9 created 1961]
 
 
EC 4.1.2.10     
Accepted name: (R)-mandelonitrile lyase
Reaction: (R)-mandelonitrile = cyanide + benzaldehyde
Other name(s): (R)-oxynitrilase; oxynitrilase; D-oxynitrilase; D-α-hydroxynitrile lyase; mandelonitrile benzaldehyde-lyase; PaHNL; AtHNL; PhaMDL; (R)-HNL; (R)-PeHNL; (R)-hydroxynitrile lyase; R-selective hydroxynitrile lyase; R-selective HNL; (R)-(+)-mandelonitrile lyase
Systematic name: (R)-mandelonitrile benzaldehyde-lyase (cyanide-forming)
Comments: A variety of enzymes from different sources and with different properties. Some are flavoproteins, others are not. Active towards a number of aromatic and aliphatic hydroxynitriles (cyanohydrins).
References:
1.  Ueatrongchit, T., Kayo, A., Komeda, H., Asano, Y. and H-Kittikun, A. Purification and characterization of a novel (R)-hydroxynitrile lyase from Eriobotrya japonica (Loquat). Biosci. Biotechnol. Biochem. 72 (2008) 1513–1522. [PMID: 18540101]
2.  Lin, G., Han, S. and Li, Z. Enzymic synthesis of (R)-cyanohydrins by three (R)-oxynitrilase sources in micro-aqueous organic medium. Tetrahedron 55 (1999) 3531–3540.
3.  de Gonzalo, G., Brieva, R. and Gotor, V. (R)-Oxynitrilase-catalyzed transformation of ω-hydroxyalkanals. J. Mol. Catal. B 19-20 (2002) 223–230.
4.  Ueatrongchit, T., Tamura, K., Ohmiya, T., H-Kittikun, A. and Asano, Y. Hydroxynitrile lyase from Passiflora edulis. Purification, characteristics and application in asymmetric synthesis of (R)-mandelonitrile. Enzyme Microb. Technol. 46 (2010) 456–465. [PMID: 25919621]
5.  Andexer, J., von Langermann, J., Mell, A., Bocola, M., Kragl, U., Eggert, T. and Pohl, M. An R-selective hydroxynitrile lyase from Arabidopsis thaliana with an α/β-hydrolase fold. Angew. Chem. Int. Ed. Engl. 46 (2007) 8679–8681. [PMID: 17907254]
6.  Guterl, J.K., Andexer, J.N., Sehl, T., von Langermann, J., Frindi-Wosch, I., Rosenkranz, T., Fitter, J., Gruber, K., Kragl, U., Eggert, T. and Pohl, M. Uneven twins: comparison of two enantiocomplementary hydroxynitrile lyases with α/β-hydrolase fold. J. Biotechnol. 141 (2009) 166–173. [PMID: 19433222]
[EC 4.1.2.10 created 1961, modified 1999, modified 2011]
 
 
EC 4.1.2.11     
Accepted name: hydroxymandelonitrile lyase
Reaction: (S)-4-hydroxymandelonitrile = cyanide + 4-hydroxybenzaldehyde
Other name(s): hydroxynitrile lyase; oxynitrilase; Sorghum hydroxynitrile lyase; (S)-4-hydroxymandelonitrile hydroxybenzaldehyde-lyase
Systematic name: (S)-4-hydroxymandelonitrile 4-hydroxybenzaldehyde-lyase (cyanide-forming)
Comments: Does not accept aliphatic hydroxynitriles, unlike EC 4.1.2.10 (mandelonitrile lyase), EC 4.1.2.46 [aliphatic (R)-hydroxynitrile lyase] and EC 4.1.2.47 [(S)-hydroxynitrile ketone-lyase (cyanide forming)].
References:
1.  Bové, C. and Conn, E.E. Metabolism of aromatic compounds in higher plants. II. Purification and properties of the oxynitrilase of Sorghum vulgare. J. Biol. Chem. 236 (1961) 207–210.
2.  Seely, M.K., Criddle, R.S. and Conn, E.E. The metabolism of aromatic compounds in higher plants. 8. On the requirement of hydroxynitrile lyase for flavin. J. Biol. Chem. 241 (1966) 4457–4462. [PMID: 5922969]
[EC 4.1.2.11 created 1965, modified 1999]
 
 
EC 4.1.2.12     
Accepted name: 2-dehydropantoate aldolase
Reaction: 2-dehydropantoate = 3-methyl-2-oxobutanoate + formaldehyde
Glossary: pantoate = 2,4-dihydroxy-3,3-dimethylbutanoate
Other name(s): ketopantoaldolase; 2-dehydropantoate formaldehyde-lyase
Systematic name: 2-dehydropantoate formaldehyde-lyase (3-methyl-2-oxobutanoate-forming)
References:
1.  McIntosh, E.N., Purko, M. and Wood, W.A. Ketopantoate formation by a hydroxymethylation enzyme from Escherichia coli. J. Biol. Chem. 228 (1957) 499–510. [PMID: 13475336]
[EC 4.1.2.12 created 1965, modified 2002]
 
 
EC 4.1.2.13     
Accepted name: fructose-bisphosphate aldolase
Reaction: D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): aldolase; fructose-1,6-bisphosphate triosephosphate-lyase; fructose diphosphate aldolase; diphosphofructose aldolase; fructose 1,6-diphosphate aldolase; ketose 1-phosphate aldolase; phosphofructoaldolase; zymohexase; fructoaldolase; fructose 1-phosphate aldolase; fructose 1-monophosphate aldolase; 1,6-diphosphofructose aldolase; SMALDO; D-fructose-1,6-bisphosphate D-glyceraldehyde-3-phosphate-lyase
Systematic name: D-fructose-1,6-bisphosphate D-glyceraldehyde-3-phosphate-lyase (glycerone-phosphate-forming)
Comments: Also acts on (3S,4R)-ketose 1-phosphates. The yeast and bacterial enzymes are zinc proteins. The enzymes increase electron-attraction by the carbonyl group, some (Class I) forming a protonated imine with it, others (Class II), mainly of microbial origin, polarizing it with a metal ion, e.g. zinc.
References:
1.  Horecker, B.L., Tsolas, O. and Lai, C.Y. Aldolases. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 7, Academic Press, New York, 1972, pp. 213–258.
2.  Alefounder, P.R., Baldwin, S.A., Perham, R.N., Short, N.J. Cloning, sequence analysis and over-expression of the gene for the class II fructose 1,6-bisphosphate aldolase of Escherichia coli. Biochem. J. 257 (1989) 529–534. [PMID: 2649077]
[EC 4.1.2.13 created 1965, modified 1999 (EC 4.1.2.7 created 1961, incorporated 1972)]
 
 
EC 4.1.2.14     
Accepted name: 2-dehydro-3-deoxy-phosphogluconate aldolase
Reaction: 2-dehydro-3-deoxy-6-phospho-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate
Other name(s): phospho-2-keto-3-deoxygluconate aldolase; KDPG aldolase; phospho-2-keto-3-deoxygluconic aldolase; 2-keto-3-deoxy-6-phosphogluconic aldolase; 2-keto-3-deoxy-6-phosphogluconate aldolase; 6-phospho-2-keto-3-deoxygluconate aldolase; ODPG aldolase; 2-oxo-3-deoxy-6-phosphogluconate aldolase; 2-keto-3-deoxygluconate-6-P-aldolase; 2-keto-3-deoxygluconate-6-phosphate aldolase; 2-dehydro-3-deoxy-D-gluconate-6-phosphate D-glyceraldehyde-3-phosphate-lyase; 2-dehydro-3-deoxy-D-gluconate-6-phosphate D-glyceraldehyde-3-phosphate-lyase (pyruvate-forming)
Systematic name: 2-dehydro-3-deoxy-6-phospho-D-gluconate D-glyceraldehyde-3-phosphate-lyase (pyruvate-forming)
Comments: The enzyme shows no activity with 2-dehydro-3-deoxy-6-phosphate-D-galactonate. cf. EC 4.1.2.55, 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase [2]. Also acts on 2-oxobutanoate [1].
References:
1.  Meloche, H.P. and Wood, W.A. Crystallization and characteristics of 2-keto-3-deoxy-6-phosphogluconic aldolase. J. Biol. Chem. 239 (1964) 3515–3518. [PMID: 14245411]
2.  Barran, L.R. and Wood, W.A. The mechanism of 2-keto-3-deoxy-6-phosphogluconate aldolase. 3. Nature of the inactivation by fluorodinitrobenzene. J. Biol. Chem. 246 (1971) 4028–4035. [PMID: 5561473]
[EC 4.1.2.14 created 1965, modified 1976, modified 2014]
 
 
EC 4.1.2.15      
Transferred entry: 2-dehydro-3-deoxy-phosphoheptonate aldolase. Now EC 2.5.1.54, 3-deoxy-7-phosphoheptulonate synthase
[EC 4.1.2.15 created 1965, modified 1976, deleted 2002]
 
 
EC 4.1.2.16      
Transferred entry: 2-dehydro-3-deoxy-phosphooctonate aldolase. Now EC 2.5.1.55, 3-deoxy-8-phosphooctulonate synthase
[EC 4.1.2.16 created 1965, deleted 2002]
 
 
EC 4.1.2.17     
Accepted name: L-fuculose-phosphate aldolase
Reaction: L-fuculose 1-phosphate = glycerone phosphate + (S)-lactaldehyde
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): L-fuculose 1-phosphate aldolase; fuculose aldolase; L-fuculose-1-phosphate lactaldehyde-lyase
Systematic name: L-fuculose-1-phosphate (S)-lactaldehyde-lyase (glycerone-phosphate-forming)
References:
1.  Ghalambor, M.A. and Heath, E.C. The biosynthesis of cell wall lipopolysaccharide in Escherichia coli. IV. Purification and properties of cytidine monophosphate 3-deoxy-D-manno-octulosonate synthetase. J. Biol. Chem. 241 (1966) 3216–3221. [PMID: 5330266]
2.  Dreyer, M.K. and Schulz, G.E. The spatial structure of the class II L-fuculose-1-phosphate aldolase from Escherichia coli. J. Mol. Biol. 231 (1993) 549–553. [PMID: 8515438]
3.  Dreyer, M.K. and Schulz, G.E. Catalytic mechanism of the metal-dependent fuculose aldolase from Escherichia coli as derived from the structure. J. Mol. Biol. 259 (1996) 458–466. [PMID: 8676381]
[EC 4.1.2.17 created 1965]
 
 
EC 4.1.2.18     
Accepted name: 2-dehydro-3-deoxy-L-pentonate aldolase
Reaction: 2-dehydro-3-deoxy-L-pentonate = pyruvate + glycolaldehyde
Other name(s): 2-keto-3-deoxy-L-pentonate aldolase; 2-keto-3-deoxy-L-arabonate aldolase; 2-keto-3-deoxy-D-xylonate aldolase; 3-deoxy-D-pentulosonic acid aldolase; 2-dehydro-3-deoxy-L-pentonate glycolaldehyde-lyase
Systematic name: 2-dehydro-3-deoxy-L-pentonate glycolaldehyde-lyase (pyruvate-forming)
References:
1.  Dahms, A.S. and Anderson, R.L. 2-Keto-3-deoxy-L-arabonate aldolase and its role in a new pathway of L-arabinose degradation. Biochem. Biophys. Res. Commun. 36 (1969) 809–814. [PMID: 5808295]
[EC 4.1.2.18 created 1972, modified 1976]
 
 
EC 4.1.2.19     
Accepted name: rhamnulose-1-phosphate aldolase
Reaction: L-rhamnulose 1-phosphate = glycerone phosphate + (S)-lactaldehyde
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): rhamnulose phosphate aldolase; L-rhamnulose 1-phosphate aldolase; L-rhamnulose-phosphate aldolase; L-rhamnulose-1-phosphate lactaldehyde-lyase
Systematic name: L-rhamnulose-1-phosphate (S)-lactaldehyde-lyase (glycerone-phosphate-forming)
References:
1.  Chiu, T.-H. and Feingold, D.S. L-Rhamnulose 1-phosphate aldolase from Escherichia coli. Crystallization and properties. Biochemistry 8 (1969) 98–108. [PMID: 4975916]
2.  Sawada, H. and Takagi, Y. The metabolism of L-rhamnose in Escherichia coli. 3. L-Rhamulose-phosphate aldolase. Biochim. Biophys. Acta 92 (1964) 26–32. [PMID: 14243785]
[EC 4.1.2.19 created 1972]
 
 
EC 4.1.2.20     
Accepted name: 2-dehydro-3-deoxyglucarate aldolase
Reaction: 2-dehydro-3-deoxy-D-glucarate = pyruvate + 2-hydroxy-3-oxopropanoate
Glossary: 2-hydroxy-3-oxopropanoate = tartronate semialdehyde
Other name(s): 2-keto-3-deoxyglucarate aldolase; α-keto-β-deoxy-D-glucarate aldolase; 2-dehydro-3-deoxy-D-glucarate tartronate-semialdehyde-lyase; 2-dehydro-3-deoxy-D-glucarate tartronate-semialdehyde-lyase (pyruvate-forming)
Systematic name: 2-dehydro-3-deoxy-D-glucarate 2-hydroxy-3-oxopropanoate-lyase (pyruvate-forming)
References:
1.  Fish, D.C. and Blumenthal, H.J. 2-Keto-3-deoxy-D-glucarate aldolase. Methods Enzymol. 9 (1966) 529–534.
[EC 4.1.2.20 created 1961 as EC 4.1.2.8, transferred 1972 to EC 4.1.2.20]
 
 
EC 4.1.2.21     
Accepted name: 2-dehydro-3-deoxy-6-phosphogalactonate aldolase
Reaction: 2-dehydro-3-deoxy-6-phospho-D-galactonate = pyruvate + D-glyceraldehyde 3-phosphate
Other name(s): 6-phospho-2-keto-3-deoxygalactonate aldolase; phospho-2-keto-3-deoxygalactonate aldolase; 2-keto-3-deoxy-6-phosphogalactonic aldolase; phospho-2-keto-3-deoxygalactonic aldolase; 2-keto-3-deoxy-6-phosphogalactonic acid aldolase; (KDPGal)aldolase; 2-dehydro-3-deoxy-D-galactonate-6-phosphate D-glyceraldehyde-3-phosphate-lyase; 2-dehydro-3-deoxy-D-galactonate-6-phosphate D-glyceraldehyde-3-phosphate-lyase (pyruvate-forming)
Systematic name: 2-dehydro-3-deoxy-6-phospho-D-galactonate D-glyceraldehyde-3-phospho-lyase (pyruvate-forming)
Comments: The enzyme catalyses the last reaction in a D-galactose degradation pathway. cf. EC 4.1.2.55, 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase.
References:
1.  Shuster, C.W. 2-Keto-3-deoxy-6-phosphogalactonic acid aldolase. Methods Enzymol. 9 (1966) 524–528.
[EC 4.1.2.21 created 1972, modified 2014]
 
 
EC 4.1.2.22     
Accepted name: fructose-6-phosphate phosphoketolase
Reaction: D-fructose 6-phosphate + phosphate = acetyl phosphate + D-erythrose 4-phosphate + H2O
Other name(s): D-fructose-6-phosphate D-erythrose-4-phosphate-lyase (phosphate-acetylating)
Systematic name: D-fructose-6-phosphate D-erythrose-4-phosphate-lyase (adding phosphate; acetyl-phosphate-forming)
Comments: Also acts on D-xylulose 5-phosphate.
References:
1.  Schramm, M., Klybas, V. and Racker, E. Phospholytic cleavage of fructose-6-phosphate by fructose-6-phosphate phosphoketolase from Acetobacter xylinum. J. Biol. Chem. 233 (1958) 1283–1288. [PMID: 13610828]
[EC 4.1.2.22 created 1972]
 
 
EC 4.1.2.23     
Accepted name: 3-deoxy-D-manno-octulosonate aldolase
Reaction: 3-deoxy-D-manno-octulosonate = pyruvate + D-arabinose
Other name(s): 2-keto-3-deoxyoctonate aldolase; KDOaldolase; 3-deoxyoctulosonic aldolase; 2-keto-3-deoxyoctonic aldolase; 3-deoxy-D-manno-octulosonic aldolase; 3-deoxy-D-manno-octulosonate D-arabinose-lyase
Systematic name: 3-deoxy-D-manno-octulosonate D-arabinose-lyase (pyruvate-forming)
References:
1.  Ghalambor, M.A. and Heath, E.C. The biosynthesis of cell wall lipopolysaccharide in Escherichia coli. V. Purification and properties of 3-deoxy-D-manno-octulosonate aldolase. J. Biol. Chem. 241 (1966) 3222–3227. [PMID: 5912115]
[EC 4.1.2.23 created 1972]
 
 
EC 4.1.2.24     
Accepted name: dimethylaniline-N-oxide aldolase
Reaction: N,N-dimethylaniline N-oxide = N-methylaniline + formaldehyde
Other name(s): microsomal oxidase II; microsomal N-oxide dealkylase; N,N-dimethylaniline-N-oxide formaldehyde-lyase
Systematic name: N,N-dimethylaniline-N-oxide formaldehyde-lyase (N-methylaniline-forming)
Comments: Acts on various N,N-dialkylarylamides.
References:
1.  Machinist, J.M., Orme-Johnson, W.H. and Ziegler, D.M. Microsomal oxidases. II. Properties of a pork liver microsomal N-oxide dealkylase. Biochemistry 5 (1966) 2939–2943. [PMID: 5961882]
[EC 4.1.2.24 created 1972]
 
 
EC 4.1.2.25     
Accepted name: dihydroneopterin aldolase
Reaction: 7,8-dihydroneopterin = 6-(hydroxymethyl)-7,8-dihydropterin + glycolaldehyde
Other name(s): 7,8-dihydroneopterin aldolase; 2-amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7,8-dihydropteridine glycolaldehyde-lyase; 2-amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7,8-dihydropteridine glycolaldehyde-lyase (2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine-forming); DHNA; mptD (gene name); folB (gene name)
Systematic name: 7,8-dihydroneopterin glycolaldehyde-lyase [6-(hydroxymethyl)-7,8-dihydropterin-forming]
Comments: The enzyme participates in folate (in bacteria, plants and fungi) and methanopterin (in archaea) biosynthesis. The enzymes from the bacterium Escherichia coli and the plant Arabidopsis thaliana also catalyse the epimerisation of the 2′ hydroxy-group (EC 5.1.99.8, 7,8-dihydroneopterin epimerase) [2,3]. The enzyme from the bacterium Mycobacterium tuberculosis is trifunctional and also catalyses EC 5.1.99.8 and EC 1.13.11.81, 7,8-dihydroneopterin oxygenase [6]. The enzyme from the yeast Saccharomyces cerevisiae also catalyses the two subsequent steps in the folate biosynthesis pathway - EC 2.7.6.3, 2-amino-4-hydroxy-6-(hydroxymethyl)dihydropteridine diphosphokinase, and EC 2.5.1.15, dihydropteroate synthase [4].
References:
1.  Mathis, J.B. and Brown, G.M. The biosynthesis of folic acid. XI. Purification and properties of dihydroneopterin aldolase. J. Biol. Chem. 245 (1970) 3015–3025. [PMID: 4912541]
2.  Haussmann, C., Rohdich, F., Schmidt, E., Bacher, A. and Richter, G. Biosynthesis of pteridines in Escherichia coli. Structural and mechanistic similarity of dihydroneopterin-triphosphate epimerase and dihydroneopterin aldolase. J. Biol. Chem. 273 (1998) 17418–17424. [PMID: 9651328]
3.  Goyer, A., Illarionova, V., Roje, S., Fischer, M., Bacher, A. and Hanson, A.D. Folate biosynthesis in higher plants. cDNA cloning, heterologous expression, and characterization of dihydroneopterin aldolases. Plant Physiol. 135 (2004) 103–111. [PMID: 15107504]
4.  Güldener, U., Koehler, G.J., Haussmann, C., Bacher, A., Kricke, J., Becher, D. and Hegemann, J.H. Characterization of the Saccharomyces cerevisiae Fol1 protein: starvation for C1 carrier induces pseudohyphal growth. Mol. Biol. Cell 15 (2004) 3811–3828. [PMID: 15169867]
5.  Czekster, C.M. and Blanchard, J.S. One substrate, five products: reactions catalyzed by the dihydroneopterin aldolase from Mycobacterium tuberculosis. J. Am. Chem. Soc. 134 (2012) 19758–19771. [PMID: 23150985]
6.  Wang, Y., Xu, H., Grochowski, L.L. and White, R.H. Biochemical characterization of a dihydroneopterin aldolase used for methanopterin biosynthesis in methanogens. J. Bacteriol. 196 (2014) 3191–3198. [PMID: 24982305]
7.  Blaszczyk, J., Lu, Z., Li, Y., Yan, H. and Ji, X. Crystallographic and molecular dynamics simulation analysis of Escherichia coli dihydroneopterin aldolase. Cell Biosci 4:52 (2014). [PMID: 25264482]
[EC 4.1.2.25 created 1972, modified 2015]
 
 
EC 4.1.2.26     
Accepted name: phenylserine aldolase
Reaction: L-threo-3-phenylserine = glycine + benzaldehyde
Other name(s): L-threo-3-phenylserine benzaldehyde-lyase
Systematic name: L-threo-3-phenylserine benzaldehyde-lyase (glycine-forming)
Comments: A pyridoxal-phosphate protein.
References:
1.  Bruns, F.H. and Fiedler, L. Enzymatic cleavage and synthesis of L-threo-β-phenylserine and L-erythro-β-phenylserine. Nature 181 (1958) 1533–1534. [PMID: 13566053]
[EC 4.1.2.26 created 1972]
 
 
EC 4.1.2.27     
Accepted name: sphinganine-1-phosphate aldolase
Reaction: sphinganine 1-phosphate = phosphoethanolamine + palmitaldehyde
Other name(s): dihydrosphingosine 1-phosphate aldolase; sphinganine-1-phosphate alkanal-lyase; sphinganine-1-phosphate lyase; sphinganine-1-phosphate palmitaldehyde-lyase
Systematic name: sphinganine-1-phosphate palmitaldehyde-lyase (phosphoethanolamine-forming)
Comments: A pyridoxal-phosphate protein.
References:
1.  Stoffel, W., Le Kim, D. and Sticht, G. Distribution and properties of dihydrosphingosine-1-phosphate aldolase (sphinganine-1-phosphate alkanal-lyase). Hoppe-Seyler's Z. Physiol. Chem. 350 (1969) 1233–1241. [PMID: 5389296]
[EC 4.1.2.27 created 1972]
 
 
EC 4.1.2.28     
Accepted name: 2-dehydro-3-deoxy-D-pentonate aldolase
Reaction: 2-dehydro-3-deoxy-D-pentonate = pyruvate + glycolaldehyde
Other name(s): 2-keto-3-deoxy-D-pentonate aldolase; 3-deoxy-D-pentulosonic acid aldolase; 2-dehydro-3-deoxy-D-pentonate glycolaldehyde-lyase
Systematic name: 2-dehydro-3-deoxy-D-pentonate glycolaldehyde-lyase (pyruvate-forming)
References:
1.  Dahms, A.S. 3-Deoxy-D-pentulosonic acid aldolase and its role in a new pathway of D-xylose degradation. Biochem. Biophys. Res. Commun. 60 (1974) 1433–1439. [PMID: 4423285]
2.  Dahms, A.S. and Donald, A. 2-Keto-3-deoxy-D-xylonate aldolase (3-deoxy-D-pentulosonic acid aldolase). Methods Enzymol. 90 (1982) 269–272. [PMID: 7154955]
[EC 4.1.2.28 created 1976]
 
 
EC 4.1.2.29     
Accepted name: 5-dehydro-2-deoxyphosphogluconate aldolase
Reaction: 5-dehydro-2-deoxy-D-gluconate 6-phosphate = glycerone phosphate + malonate semialdehyde
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): phospho-5-keto-2-deoxygluconate aldolase; 5-dehydro-2-deoxy-D-gluconate-6-phosphate malonate-semialdehyde-lyase
Systematic name: 5-dehydro-2-deoxy-D-gluconate-6-phosphate malonate-semialdehyde-lyase (glycerone-phosphate-forming)
References:
1.  Anderson, W.A. and Magasanik, B. The pathway of myo-inositol degradation in Aerobacter aerogenes. Conversion of 2-deoxy-5-keto-D-gluconic acid to glycolytic intermediates. J. Biol. Chem. 246 (1971) 5662–5675. [PMID: 4328832]
[EC 4.1.2.29 created 1976]
 
 
EC 4.1.2.30      
Transferred entry: 17α-hydroxyprogesterone aldolase. Now EC 1.14.14.32, 17α-hydroxyprogesterone deacetylase
[EC 4.1.2.30 created 1976, deleted 2016]
 
 
EC 4.1.2.31      
Deleted entry:  2-oxo-4-hydroxyglutarate aldolase. Now included with EC 4.1.3.16 4-hydroxy-2-oxoglutarate aldolase
[EC 4.1.2.31 created 1978, deleted 1982]
 
 
EC 4.1.2.32     
Accepted name: trimethylamine-oxide aldolase
Reaction: trimethylamine N-oxide = dimethylamine + formaldehyde
Other name(s): trimethylamine N-oxide formaldehyde-lyase; trimethylamine N-oxide aldolase; trimethylamine N-oxide demethylase; trimethylamine-N-oxide formaldehyde-lyase
Systematic name: trimethylamine-N-oxide formaldehyde-lyase (dimethylamine-forming)
References:
1.  Large, P.J. Non-oxidative demethylation of trimethyl N-oxide by Pseudomonas aminovorans. FEBS Lett. 18 (1971) 297–300. [PMID: 11946146]
2.  Myers, P.A. and Zatman, L.J. The metabolism of trimethylamine N-oxide by Bacillus PM6. Biochem. J. 121 (1971) 10. [PMID: 5116524]
[EC 4.1.2.32 created 1978]
 
 
EC 4.1.2.33     
Accepted name: fucosterol-epoxide lyase
Reaction: (24R,241R)-fucosterol epoxide = desmosterol + acetaldehyde
Glossary: (24R,241R)-fucosterol epoxide = (3β,24R,28R)-24,28-epoxystigmast-5-en-3-ol
Other name(s): (24R,24′R)-fucosterol-epoxide acetaldehyde-lyase; (24R,24′R)-fucosterol-epoxide acetaldehyde-lyase (desmosterol-forming)
Systematic name: (24R,241R)-fucosterol-epoxide acetaldehyde-lyase (desmosterol-forming)
Comments: The insect enzyme is involved in the conversion of sitosterol into cholesterol.
References:
1.  Prestwich, G.D., Angelastro, M., De Palma, A. and Perino, M.A. Fucosterol epoxide lyase of insects: synthesis of labeled substrates and development of a partition assay. Anal. Biochem. 151 (1985) 315–326. [PMID: 3913328]
[EC 4.1.2.33 created 1989, modified 2013]
 
 
EC 4.1.2.34     
Accepted name: 4-(2-carboxyphenyl)-2-oxobut-3-enoate aldolase
Reaction: (3Z)-4-(2-carboxyphenyl)-2-oxobut-3-enoate + H2O = 2-formylbenzoate + pyruvate
Other name(s): 2′-carboxybenzalpyruvate aldolase; (3E)-4-(2-carboxyphenyl)-2-oxobut-3-enoate 2-carboxybenzaldehyde-lyase; (3Z)-4-(2-carboxyphenyl)-2-oxobut-3-enoate 2-formylbenzoate-lyase
Systematic name: (3Z)-4-(2-carboxyphenyl)-2-oxobut-3-enoate 2-formylbenzoate-lyase (pyruvate-forming)
Comments: Involved, with EC 1.13.11.38 (1-hydroxy-2-naphthoate 1,2-dioxygenase), in the metabolism of phenanthrene in bacteria.
References:
1.  Barnsley, E.A. Phthalate pathway of phenanthrene metabolism: formation of 2′-carboxybenzalpyruvate. J. Bacteriol. 154 (1983) 113–117. [PMID: 6833175]
[EC 4.1.2.34 created 1989]
 
 
EC 4.1.2.35     
Accepted name: propioin synthase
Reaction: 4-hydroxy-3-hexanone = 2 propanal
Other name(s): 4-hydroxy-3-hexanone aldolase; 4-hydroxy-3-hexanone propanal-lyase
Systematic name: 4-hydroxy-3-hexanone propanal-lyase (propanal-forming)
References:
1.  Morimoto, S., Azuma, K., Oshima, T. and Sakamoto, M. Purification and properties of a new enzyme, propioin synthase in bakers' yeast which forms propioin from propionaldehyde. J. Ferment. Technol. 66 (1988) 7–12.
[EC 4.1.2.35 created 1990]
 
 
EC 4.1.2.36     
Accepted name: lactate aldolase
Reaction: (S)-lactate = formate + acetaldehyde
Other name(s): lactate synthase; (S)-lactate acetaldehyde-lyase
Systematic name: (S)-lactate acetaldehyde-lyase (formate-forming)
References:
1.  Gulyi, M.F. and Silonova, N.V. [Various metabolic reactions of formate in animal tissues.] Ukr. Biokhim. Zh. 59 (1987) 29–35. [PMID: 3629727] (in Russian)
[EC 4.1.2.36 created 1990]
 
 
EC 4.1.2.37      
Deleted entry: hydroxynitrilase. Now covered by EC 4.1.2.46 [aliphatic (R)-hydroxynitrile lyase] and EC 4.1.2.47 [(S)-hydroxynitrile ketone-lyase (cyanide forming)]
[EC 4.1.2.37 created 1992 (EC 4.1.2.39 created 1999, incorporated 2007), deleted 2011]
 
 
EC 4.1.2.38     
Accepted name: benzoin aldolase
Reaction: 2-hydroxy-1,2-diphenylethanone = 2 benzaldehyde
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
benzoin = 2-hydroxy-1,2-diphenylethanone
Other name(s): benzaldehyde lyase; 2-hydroxy-1,2-diphenylethanone benzaldehyde-lyase
Systematic name: 2-hydroxy-1,2-diphenylethanone benzaldehyde-lyase (benzaldehyde-forming)
Comments: A thiamine-diphosphate protein.
References:
1.  González, B. and Vicuñna, R. Benzaldehyde lyase, a novel thiamine PPi-requiring enzyme, from Pseudomonas fluorescens biovar I. J. Bacteriol. 171 (1989) 2401–2405. [PMID: 2496105]
[EC 4.1.2.38 created 1992]
 
 
EC 4.1.2.39      
Deleted entry: hydroxynitrilase. The enzyme is identical to EC 4.1.2.37, hydroxynitrilase
[EC 4.1.2.39 created 1999, deleted 2007]
 
 
EC 4.1.2.40     
Accepted name: tagatose-bisphosphate aldolase
Reaction: D-tagatose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): D-tagatose-1,6-bisphosphate triosephosphate lyase
Systematic name: D-tagatose 1,6-bisphosphate D-glyceraldehyde-3-phosphate-lyase (glycerone-phosphate-forming)
Comments: Enzyme activity is stimulated by certain divalent cations. It is involved in the tagatose 6-phosphate pathway of lactose catabolism in bacteria.
References:
1.  Anderson, R.L. and Markwell, J.P. D-Tagatose-1,6-bisphosphate aldolase (class II) from Klebsiella pneumoniae. Methods Enzymol. 90 (1982) 232–234. [PMID: 6759854]
2.  Van Rooijen, R.J., Van Schalkwijk, S., De Vos, W.M. Molecular cloning, characterization, and nucleotide sequence of the tagatose 6-phosphate pathway gene cluster of the lactose operon of Lactococcus lactis. J. Biol. Chem. 266 (1991) 7176–7181. [PMID: 1901863]
[EC 4.1.2.40 created 1999]
 
 
EC 4.1.2.41      
Transferred entry: vanillin synthase. Now included with EC 4.1.2.61, feruloyl-CoA hydratase/lyase
[EC 4.1.2.41 created 2000, deleted 2019]
 
 
EC 4.1.2.42     
Accepted name: D-threonine aldolase
Reaction: (1) D-threonine = glycine + acetaldehyde
(2) D-allothreonine = glycine + acetaldehyde
Glossary: D-threonine = (2R,3S)-2-amino-3-hydroxybutanoic acid
D-allothreonine = (2R,3R)-2-amino-3-hydroxybutanoic acid
Other name(s): D-TA; DTA; low specificity D-TA; low specificity D-threonine aldolase
Systematic name: D-threonine acetaldehyde-lyase (glycine-forming)
Comments: A pyridoxal-phosphate protein that is activated by divalent metal cations (e.g. Co2+, Ni2+, Mn2+ or Mg2+) [1,2]. The reaction is reversible, which can lead to the interconversion of D-threonine and D-allothreonine [1]. Several other D-β-hydroxy-α-amino acids, such as D-β-phenylserine, D-β-hydroxy-α-aminovaleric acid and D-β-3,4-dihydroxyphenylserine, can also act as substrate [1].
References:
1.  Kataoka, M., Ikemi, M., Morikawa, T., Miyoshi, T., Nishi, K., Wada, M., Yamada, H. and Shimizu, S. Isolation and characterization of D-threonine aldolase, a pyridoxal-5′-phosphate-dependent enzyme from Arthrobacter sp. DK-38. Eur. J. Biochem. 248 (1997) 385–393. [PMID: 9346293]
2.  Liu, J.Q., Dairi, T., Itoh, N., Kataoka, M., Shimizu, S. and Yamada, H. A novel metal-activated pyridoxal enzyme with a unique primary structure, low specificity D-threonine aldolase from Arthrobacter sp. Strain DK-38. Molecular cloning and cofactor characterization. J. Biol. Chem. 273 (1998) 16678–16685. [PMID: 9642221]
3.  Liu, J.Q., Odani, M., Dairi, T., Itoh, N., Shimizu, S. and Yamada, H. A new route to L-threo-3-[4-(methylthio)phenylserine], a key intermediate for the synthesis of antibiotics: recombinant low-specificity D-threonine aldolase-catalyzed stereospecific resolution. Appl. Microbiol. Biotechnol. 51 (1999) 586–591. [PMID: 10390816]
4.  Liu, J.Q., Odani, M., Yasuoka, T., Dairi, T., Itoh, N., Kataoka, M., Shimizu, S. and Yamada, H. Gene cloning and overproduction of low-specificity D-threonine aldolase from Alcaligenes xylosoxidans and its application for production of a key intermediate for parkinsonism drug. Appl. Microbiol. Biotechnol. 54 (2000) 44–51. [PMID: 10952004]
5.  Liu, J.Q., Dairi, T., Itoh, N., Kataoka, M., Shimizu, S. and Yamada, H. Diversity of microbial threonine aldolases and their application. J. Mol. Catal. B 10 (2000) 107–115.
6.  Paiardini, A., Contestabile, R., D'Aguanno, S., Pascarella, S. and Bossa, F. Threonine aldolase and alanine racemase: novel examples of convergent evolution in the superfamily of vitamin B6-dependent enzymes. Biochim. Biophys. Acta 1647 (2003) 214–219. [PMID: 12686135]
[EC 4.1.2.42 created 2007]
 
 
EC 4.1.2.43     
Accepted name: 3-hexulose-6-phosphate synthase
Reaction: D-arabino-hex-3-ulose 6-phosphate = D-ribulose 5-phosphate + formaldehyde
Other name(s): D-arabino-3-hexulose 6-phosphate formaldehyde-lyase; 3-hexulosephosphate synthase; 3-hexulose phosphate synthase; HPS
Systematic name: D-arabino-hex-3-ulose-6-phosphate formaldehyde-lyase (D-ribulose-5-phosphate-forming)
Comments: Requires Mg2+ or Mn2+ for maximal activity [1]. The enzyme is specific for D-ribulose 5-phosphate as substrate as ribose 5-phosphate, xylulose 5-phosphate, allulose 6-phosphate and fructose 6-phosphate cannot act as substrate. In addition to formaldehyde, the enzyme can also use glycolaldehyde and methylglyoxal [7]. This enzyme, along with EC 5.3.1.27, 6-phospho-3-hexuloisomerase, plays a key role in the ribulose-monophosphate cycle of formaldehyde fixation, which is present in many microorganisms that are capable of utilizing C1-compounds [1]. The hyperthermophilic and anaerobic archaeon Pyrococcus horikoshii OT3 constitutively produces a bifunctional enzyme that sequentially catalyses the reactions of this enzyme and EC 5.3.1.27, 6-phospho-3-hexuloisomerase [6]. This enzyme is a member of the orotidine 5′-monophosphate decarboxylase (OMPDC) suprafamily [5].
References:
1.  Ferenci, T., Strøm, T. and Quayle, J.R. Purification and properties of 3-hexulose phosphate synthase and phospho-3-hexuloisomerase from Methylococcus capsulatus. Biochem. J. 144 (1974) 477–486. [PMID: 4219834]
2.  Kato, N., Ohashi, H., Tani, Y. and Ogata, K. 3-Hexulosephosphate synthase from Methylomonas aminofaciens 77a. Purification, properties and kinetics. Biochim. Biophys. Acta 523 (1978) 236–244. [PMID: 564713]
3.  Yanase, H., Ikeyama, K., Mitsui, R., Ra, S., Kita, K., Sakai, Y. and Kato, N. Cloning and sequence analysis of the gene encoding 3-hexulose-6-phosphate synthase from the methylotrophic bacterium, Methylomonas aminofaciens 77a, and its expression in Escherichia coli. FEMS Microbiol. Lett. 135 (1996) 201–205. [PMID: 8595859]
4.  Yurimoto, H., Kato, N. and Sakai, Y. Assimilation, dissimilation, and detoxification of formaldehyde, a central metabolic intermediate of methylotrophic metabolism. Chem. Rec. 5 (2005) 367–375. [PMID: 16278835]
5.  Kato, N., Yurimoto, H. and Thauer, R.K. The physiological role of the ribulose monophosphate pathway in bacteria and archaea. Biosci. Biotechnol. Biochem. 70 (2006) 10–21. [PMID: 16428816]
6.  Orita, I., Yurimoto, H., Hirai, R., Kawarabayasi, Y., Sakai, Y. and Kato, N. The archaeon Pyrococcus horikoshii possesses a bifunctional enzyme for formaldehyde fixation via the ribulose monophosphate pathway. J. Bacteriol. 187 (2005) 3636–3642. [PMID: 15901685]
7.  Kato, N., Miyamoto, N., Shimao, M. and Sakazawa, C. 3-Hexulose phosphate pynthase from a new facultative methylotroph, Mycobacterium gastri MB19. Agric. Biol. Chem. 52 (1988) 2659–2661.
[EC 4.1.2.43 created 2008]
 
 
EC 4.1.2.44     
Accepted name: 2,3-epoxybenzoyl-CoA dihydrolase
Reaction: 2,3-epoxy-2,3-dihydrobenzoyl-CoA + 2 H2O = (3Z)-6-oxohex-3-enoyl-CoA + formate
Glossary: (3Z)-6-oxohex-3-enoyl-CoA = 3,4-didehydroadipyl-CoA semialdehyde
Other name(s): 2,3-dihydro-2,3-dihydroxybenzoyl-CoA lyase/hydrolase (deformylating); BoxC; dihydrodiol transforming enzyme; benzoyl-CoA oxidation component C; 2,3-dihydro-2,3-dihydroxybenzoyl-CoA 3,4-didehydroadipyl-CoA semialdehyde-lyase (formate-forming); benzoyl-CoA-dihydrodiol lyase (incorrect); 2,3-dihydro-2,3-dihydroxybenzoyl-CoA 3,4-didehydroadipyl-CoA-semialdehyde-lyase (formate-forming)
Systematic name: 2,3-epoxy-2,3-dihydrobenzoyl-CoA (3Z)-6-oxohex-3-enoyl-CoA-lyase (formate-forming)
Comments: The enzyme is involved in the aerobic benzoyl-CoA catabolic pathway of the bacterium Azoarcus evansii. The enzyme converts 2,3-epoxy-2,3-dihydrobenzoyl-CoA to its oxepin form prior to the ring-opening and the formation of a dialdehyde intermediate.
References:
1.  Gescher, J., Eisenreich, W., Worth, J., Bacher, A. and Fuchs, G. Aerobic benzoyl-CoA catabolic pathway in Azoarcus evansii: studies on the non-oxygenolytic ring cleavage enzyme. Mol. Microbiol. 56 (2005) 1586–1600. [PMID: 15916608]
2.  Rather, L.J., Knapp, B., Haehnel, W. and Fuchs, G. Coenzyme A-dependent aerobic metabolism of benzoate via epoxide formation. J. Biol. Chem. 285 (2010) 20615–20624. [PMID: 20452977]
[EC 4.1.2.44 created 2010, modified 2015]
 
 
EC 4.1.2.45     
Accepted name: trans-o-hydroxybenzylidenepyruvate hydratase-aldolase
Reaction: (3E)-4-(2-hydroxyphenyl)-2-oxobut-3-enoate + H2O = salicylaldehyde + pyruvate
Glossary: (3E)-4-(2-hydroxyphenyl)-2-oxobut-3-enoate = (E)-2′-hydroxybenzylidenepyruvate
salicylaldehyde = 2-hydroxybenzaldehyde
Other name(s): 2′-hydroxybenzalpyruvate aldolase; NsaE; tHBPA hydratase-aldolase
Systematic name: (3E)-4-(2-hydroxyphenyl)-2-oxobut-3-enoate hydro-lyase
Comments: This enzyme is involved in naphthalene degradation. The enzyme catalyses a retro-aldol reaction in vitro, and it accepts a broad range of aldehydes and 4-substituted 2-oxobut-3-enoates as substrates [4].
References:
1.  Kuhm, A.E., Knackmuss, H.J. and Stolz, A. Purification and properties of 2′-hydroxybenzalpyruvate aldolase from a bacterium that degrades naphthalenesulfonates. J. Biol. Chem. 268 (1993) 9484–9489. [PMID: 8486638]
2.  Keck, A., Conradt, D., Mahler, A., Stolz, A., Mattes, R. and Klein, J. Identification and functional analysis of the genes for naphthalenesulfonate catabolism by Sphingomonas xenophaga BN6. Microbiology 152 (2006) 1929–1940. [PMID: 16804169]
3.  Eaton, R.W. Organization and evolution of naphthalene catabolic pathways: sequence of the DNA encoding 2-hydroxychromene-2-carboxylate isomerase and trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from the NAH7 plasmid. J. Bacteriol. 176 (1994) 7757–7762. [PMID: 8002605]
4.  Eaton, R.W. trans-o-Hydroxybenzylidenepyruvate hydratase-aldolase as a biocatalyst. Appl. Environ. Microbiol. 66 (2000) 2668–2672. [PMID: 10831455]
[EC 4.1.2.45 created 2010, modified 2011]
 
 
EC 4.1.2.46     
Accepted name: aliphatic (R)-hydroxynitrile lyase
Reaction: (2R)-2-hydroxy-2-methylbutanenitrile = cyanide + butan-2-one
Other name(s): (R)-HNL; (R)-oxynitrilase; (R)-hydroxynitrile lyase; LuHNL
Systematic name: (2R)-2-hydroxy-2-methylbutanenitrile butan-2-one-lyase (cyanide forming)
Comments: The enzyme contains Zn2+ [1]. The enzyme catalyses the stereoselective synthesis of aliphatic (R)-cyanohydrins [1]. No activity towards mandelonitrile and 4-hydroxymandelonitrile [5]. Natural substrates for the (R)-oxynitrilase from Linum usitatissimum are acetone and butan-2-one, which are the building blocks of the cyanogen glycosides in Linum, linamarin and lotaustralin, or linustatin and neolinustatin, respectively [4].
References:
1.  Trummler, K., Roos, J., Schwaneberg, U., Effenberger, F., Förster, S., Pfizenmaier, K. and Wajant, H. Expression of the Zn2+-containing hydroxynitrile lyase from flax (Linum usitatissimum) in Pichia pastoris— utilization of the recombinant enzyme for enzymatic analysis and site-directed mutagenesis. Plant Sci. 139 (1998) 19–27.
2.  Trummler, K. and Wajant, H. Molecular cloning of acetone cyanohydrin lyase from flax (Linum usitatissimum). Definition of a novel class of hydroxynitrile lyases. J. Biol. Chem. 272 (1997) 4770–4774. [PMID: 9030531]
3.  Albrecht, J., Jansen, I.and Kula, M.R. Improved purification of an (R)-oxynitrilase from Linum usitatissimum (flax) and investigation of the substrate range. Biotechnol. Appl. Biochem. 17 (1993) 191–203. [PMID: 8387315]
4.  Xu, L.-L., Singh, B.K. and Conn, E.E. Purification and characterization of acetone cyanohydrin lyase from Linum usitatissimum. Arch. Biochem. Biophys. 263 (1988) 256–263. [PMID: 3377504]
5.  Cabirol, F.L., Tan, P.L., Tay, B., Cheng, S., Hanefeld, U. and Sheldon, R.A. Linum usitatissimum hydroxynitrile lyase cross-linked enzyme aggregates: a recyclable enantioselective catalyst. Adv. Synth. Catal. 350 (2008) 2329–2338.
6.  Breithaupt, H., Pohl, M., Bönigk, W., Heim, P., Schimz, K.-L. and Kula, M.-R. Cloning and expression of (R)-hydroxynitrile lyase from Linum usitatissimum (flax). J. Mol. Catal. B 6 (1999) 315–332.
[EC 4.1.2.46 created 2011]
 
 
EC 4.1.2.47     
Accepted name: (S)-hydroxynitrile lyase
Reaction: (1) an aliphatic (S)-hydroxynitrile = cyanide + an aliphatic aldehyde or ketone
(2) an aromatic (S)-hydroxynitrile = cyanide + an aromatic aldehyde
Other name(s): (S)-cyanohydrin producing hydroxynitrile lyase; (S)-oxynitrilase; (S)-HbHNL; (S)-MeHNL; hydroxynitrile lyase; oxynitrilase; HbHNL; MeHNL; (S)-selective hydroxynitrile lyase; (S)-cyanohydrin carbonyl-lyase (cyanide forming)
Systematic name: (S)-cyanohydrin lyase (cyanide forming)
Comments: Hydroxynitrile lyases catalyses the the cleavage of hydroxynitriles into cyanide and the corresponding aldehyde or ketone. In nature the liberation of cyanide serves as a defense mechanism against herbivores and microbial attack in plants. In vitro the enzymes from Manihot esculenta and Hevea brasiliensis accept a broad range of aliphatic and aromatic carbonyl compounds as substrates and catalyse the formation of (S)-hydroxynitriles [1,10].
References:
1.  Förster, S., Roos, J., Effenberger, F., Wajant, H. and Sprauer, A. The first recombinant hydroxynitrile lyase and its application in the synthesis of (S)-cyanohydrins. Angew. Chem. Int. Ed. 35 (1996) 437–439.
2.  Bühler, H., Effenberger, F., Förster, S., Roos, J. and Wajant, H. Substrate specificity of mutants of the hydroxynitrile lyase from Manihot esculenta. ChemBioChem 4 (2003) 211–216. [PMID: 12616635]
3.  Semba, H., Dobashi, Y. and Matsui, T. Expression of hydroxynitrile lyase from Manihot esculenta in yeast and its application in (S)-mandelonitrile production using an immobilized enzyme reactor. Biosci. Biotechnol. Biochem. 72 (2008) 1457–1463. [PMID: 18540112]
4.  Avi, M., Wiedner, R.M., Griengl, H. and Schwab, H. Improvement of a stereoselective biocatalytic synthesis by substrate and enzyme engineering: 2-hydroxy-(4′-oxocyclohexyl)acetonitrile as the model. Chemistry 14 (2008) 11415–11422. [PMID: 19006143]
5.  von Langermann, J., Guterl, J.K., Pohl, M., Wajant, H. and Kragl, U. Hydroxynitrile lyase catalyzed cyanohydrin synthesis at high pH-values. Bioprocess Biosyst. Eng. 31 (2008) 155–161. [PMID: 18204865]
6.  Schmidt, A., Gruber, K., Kratky, C. and Lamzin, V.S. Atomic resolution crystal structures and quantum chemistry meet to reveal subtleties of hydroxynitrile lyase catalysis. J. Biol. Chem. 283 (2008) 21827–21836. [PMID: 18524775]
7.  Gartler, G., Kratky, C. and Gruber, K. Structural determinants of the enantioselectivity of the hydroxynitrile lyase from Hevea brasiliensis. J. Biotechnol. 129 (2007) 87–97. [PMID: 17250917]
8.  Wagner, U.G., Schall, M., Hasslacher, M., Hayn, M., Griengl, H., Schwab, H. and Kratky, C. Crystallization and preliminary X-ray diffraction studies of a hydroxynitrile lyase from Hevea brasiliensis. Acta Crystallogr. D Biol. Crystallogr. 52 (1996) 591–593. [PMID: 15299689]
9.  Schmidt, M., Herve, S., Klempier, N. and Griengl, H. Preparation of optically active cyanohydrins using the (S)-hydroxynitrile lyase from Hevea brasiliensis. Tetrahedron 52 (1996) 7833–7840.
10.  Klempier, N. and Griengl, H. Aliphatic (S)-cyanohydrins by enzyme catalyzed synthesis. Tetrahedron Lett. 34 (1993) 4769–4772.
[EC 4.1.2.47 created 2011]
 
 
EC 4.1.2.48     
Accepted name: low-specificity L-threonine aldolase
Reaction: (1) L-threonine = glycine + acetaldehyde
(2) L-allo-threonine = glycine + acetaldehyde
Other name(s): LtaE
Systematic name: L-threonine/L-allo-threonine acetaldehyde-lyase (glycine-forming)
Comments: Requires pyridoxal phosphate. The low-specificity L-threonine aldolase can act on both L-threonine and L-allo-threonine [1,2]. The enzyme from Escherichia coli can also act on L-threo-phenylserine and L-erythro-phenylserine [4]. The enzyme can also catalyse the aldol condensation of glycolaldehyde and glycine to form 4-hydroxy-L-threonine, an intermediate of pyridoxal phosphate biosynthesis [3]. Different from EC 4.1.2.5, L-threonine aldolase, and EC 4.1.2.49, L-allo-threonine aldolase.
References:
1.  Yamada, H., Kumagai, H., Nagate, T. and Yoshida, H. Crystalline threonine aldolase from Candida humicola. Biochem. Biophys. Res. Commun. 39 (1970) 53–58. [PMID: 5438301]
2.  Kumagai, H., Nagate, T., Yoshida, H. and Yamada, H. Threonine aldolase from Candida humicola. II. Purification, crystallization and properties. Biochim. Biophys. Acta 258 (1972) 779–790. [PMID: 5017702]
3.  Liu, J.Q., Nagata, S., Dairi, T., Misono, H., Shimizu, S. and Yamada, H. The GLY1 gene of Saccharomyces cerevisiae encodes a low-specific L-threonine aldolase that catalyzes cleavage of L-allo-threonine and L-threonine to glycine—expression of the gene in Escherichia coli and purification and characterization of the enzyme. Eur. J. Biochem. 245 (1997) 289–293. [PMID: 9151955]
4.  Liu, J.Q., Dairi, T., Itoh, N., Kataoka, M., Shimizu, S. and Yamada, H. Gene cloning, biochemical characterization and physiological role of a thermostable low-specificity L-threonine aldolase from Escherichia coli. Eur. J. Biochem. 255 (1998) 220–226. [PMID: 9692922]
5.  Kim, J., Kershner, J.P., Novikov, Y., Shoemaker, R.K. and Copley, S.D. Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5′-phosphate synthesis. Mol. Syst. Biol. 6:436 (2010). [PMID: 21119630]
[EC 4.1.2.48 created 2011]
 
 
EC 4.1.2.49     
Accepted name: L-allo-threonine aldolase
Reaction: L-allo-threonine = glycine + acetaldehyde
Systematic name: L-allo-threonine acetaldehyde-lyase (glycine-forming)
Comments: Requires pyridoxal phosphate. This enzyme, characterized from the bacterium Aeromonas jandaei, is specific for L-allo-threonine and can not act on either L-threonine or L-serine. Different from EC 4.1.2.5, L-threonine aldolase, and EC 4.1.2.48, low-specificity L-threonine aldolase. A previously listed enzyme with this name, EC 4.1.2.6, was deleted in 1971 after it was found to be identical to EC 2.1.2.1, glycine hydroxymethyltransferase.
References:
1.  Kataoka, M., Wada, M., Nishi, K., Yamada, H. and Shimizu, S. Purification and characterization of L-allo-threonine aldolase from Aeromonas jandaei DK-39. FEMS Microbiol. Lett. 151 (1997) 245–248. [PMID: 9228760]
[EC 4.1.2.49 created 2011]
 
 
EC 4.1.2.50     
Accepted name: 6-carboxytetrahydropterin synthase
Reaction: 7,8-dihydroneopterin 3′-triphosphate + H2O = 6-carboxy-5,6,7,8-tetrahydropterin + acetaldehyde + triphosphate
Glossary: 7,8-dihydroneopterin 3′-triphosphate = 2-amino-6-[(1S,2R)-1,2-dihydroxy-3-triphosphooxypropyl]-4-oxo-2,3,7,8-tetrahydropteridine
6-carboxy-5,6,7,8-tetrahydropterin = 2-amino-4-oxo-2,3,5,6,7,8-hexahydropteridine-6-carboxylate
Other name(s): CPH4 synthase; queD (gene name); ToyB; ykvK (gene name)
Systematic name: 7,8-dihydroneopterin 3′-triphosphate acetaldehyde-lyase (6-carboxy-5,6,7,8-tetrahydropterin and triphosphate-forming)
Comments: Binds Zn2+. Isolated from the bacteria Bacillus subtilis and Escherichia coli. The reaction is part of the biosynthesis pathway of queuosine.The enzyme from Escherichia coli can also convert 6-pyruvoyl-5,6,7,8-tetrahydropterin and sepiapterin to 6-carboxy-5,6,7,8-tetrahydropterin [2].
References:
1.  Cicmil, N. and Shi, L. Crystallization and preliminary X-ray characterization of queD from Bacillus subtilis, an enzyme involved in queuosine biosynthesis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64 (2008) 119–122. [PMID: 18259064]
2.  McCarty, R.M., Somogyi, A. and Bandarian, V. Escherichia coli QueD is a 6-carboxy-5,6,7,8-tetrahydropterin synthase. Biochemistry 48 (2009) 2301–2303. [PMID: 19231875]
[EC 4.1.2.50 created 2012]
 
 
EC 4.1.2.51     
Accepted name: 2-dehydro-3-deoxy-D-gluconate aldolase
Reaction: 2-dehydro-3-deoxy-D-gluconate = pyruvate + D-glyceraldehyde
Other name(s): Pto1279 (gene name); KDGA; KDG-specific aldolase
Systematic name: 2-dehydro-3-deoxy-D-gluconate D-glyceraldehyde-lyase (pyruvate-forming)
Comments: The enzyme from the archaeon Picrophilus torridus is involved in D-glucose and D-galactose catabolism via the nonphosphorylative variant of the Entner-Doudoroff pathway. In the direction of aldol synthesis the enzyme catalyses the formation of 2-dehydro-3-deoxy-D-gluconate and 2-dehydro-3-deoxy-D-galactonate at a similar ratio. It shows no activity with 2-dehydro-3-deoxy-D-gluconate 6-phosphate. cf. EC 4.1.2.14, 2-dehydro-3-deoxy-phosphogluconate aldolase.
References:
1.  Reher, M., Fuhrer, T., Bott, M. and Schonheit, P. The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate- specific aldolase. J. Bacteriol. 192 (2010) 964–974. [PMID: 20023024]
[EC 4.1.2.51 created 2013]
 
 
EC 4.1.2.52     
Accepted name: 4-hydroxy-2-oxoheptanedioate aldolase
Reaction: 4-hydroxy-2-oxoheptanedioate = pyruvate + succinate semialdehyde
Other name(s): 2,4-dihydroxyhept-2-enedioate aldolase; HHED aldolase; 4-hydroxy-2-ketoheptanedioate aldolase; HKHD aldolase; HpcH; HpaI; 4-hydroxy-2-oxoheptanedioate succinate semialdehyde lyase (pyruvate-forming)
Systematic name: 4-hydroxy-2-oxoheptanedioate succinate-semialdehyde-lyase (pyruvate-forming)
Comments: Requires Co2+ or Mn2+ for activity. The enzyme is also able to catalyse the aldol cleavage of 4-hydroxy-2-oxopentanoate and 4-hydroxy-2-oxohexanoate, and can use 2-oxobutanoate as carbonyl donor, with lower efficiency. In the reverse direction, is able to condense a range of aldehyde acceptors with pyruvate. The enzyme from the bacterium Escherichia coli produces a racemic mixture of (4R)- and (4S)-hydroxy-2-oxoheptanedioate [4].
References:
1.  Wang, W. and Seah, S.Y. Purification and biochemical characterization of a pyruvate-specific class II aldolase, HpaI. Biochemistry 44 (2005) 9447–9455. [PMID: 15996099]
2.  Rea, D., Fulop, V., Bugg, T.D. and Roper, D.I. Structure and mechanism of HpcH: a metal ion dependent class II aldolase from the homoprotocatechuate degradation pathway of Escherichia coli. J. Mol. Biol. 373 (2007) 866–876. [PMID: 17881002]
3.  Wang, W. and Seah, S.Y. The role of a conserved histidine residue in a pyruvate-specific class II aldolase. FEBS Lett. 582 (2008) 3385–3388. [PMID: 18775708]
4.  Wang, W., Baker, P. and Seah, S.Y.K. Comparison of two metal-dependent pyruvate aldolases related by convergent evolution: substrate specificity, kinetic mechanism, and substrate channeling. Biochemistry 49 (2010) 3774–3782. [PMID: 20364820]
[EC 4.1.2.52 created 2013]
 
 
EC 4.1.2.53     
Accepted name: 2-keto-3-deoxy-L-rhamnonate aldolase
Reaction: 2-dehydro-3-deoxy-L-rhamnonate = pyruvate + (S)-lactaldehyde
Glossary: 2-dehydro-3-deoxy-L-rhamnonate = 3,6-dideoxy-L-erythro-hex-2-ulosonate
Other name(s): KDR aldolase; 2-dehydro-3-deoxyrhamnonate aldolase; 2-keto-3-deoxy acid sugar aldolase; YfaU; 2-dehydro-3-deoxy-L-rhamnonate (S)-lactaldehyde lyase (pyruvate-forming); 2-dehydro-3-deoxy-L-rhamnonate (R)-lactaldehyde lyase (pyruvate-forming)
Systematic name: 2-dehydro-3-deoxy-L-rhamnonate (S)-lactaldehyde-lyase (pyruvate-forming)
Comments: Requires Mg2+ for activity. The enzyme can also use 2-oxo-3-deoxy-L-mannonate, 2-oxo-3-deoxy-L-lyxonate and 4-hydroxy-2-ketoheptane-1,7-dioate (HKHD) as substrates [2].
References:
1.  Rakus, J.F., Fedorov, A.A., Fedorov, E.V., Glasner, M.E., Hubbard, B.K., Delli, J.D., Babbitt, P.C., Almo, S.C. and Gerlt, J.A. Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase. Biochemistry 47 (2008) 9944–9954. [PMID: 18754693]
2.  Rea, D., Hovington, R., Rakus, J.F., Gerlt, J.A., Fulop, V., Bugg, T.D. and Roper, D.I. Crystal structure and functional assignment of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12. Biochemistry 47 (2008) 9955–9965. [PMID: 18754683]
[EC 4.1.2.53 created 2013]
 
 
EC 4.1.2.54     
Accepted name: L-threo-3-deoxy-hexylosonate aldolase
Reaction: 2-dehydro-3-deoxy-L-galactonate = pyruvate + L-glyceraldehyde
Other name(s): GAAC; LGA1
Systematic name: 2-dehydro-3-deoxy-L-galactonate L-glyceraldehyde-lyase (pyruvate-forming)
Comments: The enzyme takes part in a D-galacturonate degradation pathway in the fungi Aspergillus niger and Trichoderma reesei (Hypocrea jecorina).
References:
1.  Hilditch, S., Berghall, S., Kalkkinen, N., Penttila, M. and Richard, P. The missing link in the fungal D-galacturonate pathway: identification of the L-threo-3-deoxy-hexulosonate aldolase. J. Biol. Chem. 282 (2007) 26195–26201. [PMID: 17609199]
2.  Martens-Uzunova, E.S. and Schaap, P.J. An evolutionary conserved D-galacturonic acid metabolic pathway operates across filamentous fungi capable of pectin degradation. Fungal Genet. Biol. 45 (2008) 1449–1457. [PMID: 18768163]
[EC 4.1.2.54 created 2013]
 
 
EC 4.1.2.55     
Accepted name: 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
Reaction: (1) 2-dehydro-3-deoxy-6-phospho-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate
(2) 2-dehydro-3-deoxy-6-phospho-D-galactonate = pyruvate + D-glyceraldehyde 3-phosphate
Other name(s): 2-keto-3-deoxygluconate aldolase (ambiguous); KDGA (ambiguous)
Systematic name: 2-dehydro-3-deoxy-6-phospho-D-gluconate/2-dehydro-3-deoxy-6-phospho-D-galactonate D-glyceraldehyde-3-phosphate-lyase (pyruvate-forming)
Comments: In the archaeon Sulfolobus solfataricus the enzyme is involved in glucose and galactose catabolism via the branched variant of the Entner-Doudoroff pathway. It utilizes 2-dehydro-3-deoxy-6-phosphate-D-gluconate and 2-dehydro-3-deoxy-6-phosphate-D-galactonate with similar catalytic efficiency. In vitro the enzyme can also catalyse the cleavage of the non-phosphorylated forms 2-dehydro-3-deoxy-D-gluconate and 2-dehydro-3-deoxy-D-galactonate with much lower catalytic efficiency. cf. EC 4.1.2.21, 2-dehydro-3-deoxy-6-phosphogalactonate aldolase, and EC 4.1.2.14, 2-dehydro-3-deoxy-phosphogluconate aldolase.
References:
1.  Buchanan, C.L., Connaris, H., Danson, M.J., Reeve, C.D. and Hough, D.W. An extremely thermostable aldolase from Sulfolobus solfataricus with specificity for non-phosphorylated substrates. Biochem. J. 343 (1999) 563–570. [PMID: 10527934]
2.  Lamble, H.J., Theodossis, A., Milburn, C.C., Taylor, G.L., Bull, S.D., Hough, D.W. and Danson, M.J. Promiscuity in the part-phosphorylative Entner-Doudoroff pathway of the archaeon Sulfolobus solfataricus. FEBS Lett. 579 (2005) 6865–6869. [PMID: 16330030]
3.  Wolterink-van Loo, S., van Eerde, A., Siemerink, M.A., Akerboom, J., Dijkstra, B.W. and van der Oost, J. Biochemical and structural exploration of the catalytic capacity of Sulfolobus KDG aldolases. Biochem. J. 403 (2007) 421–430. [PMID: 17176250]
[EC 4.1.2.55 created 2014]
 
 
EC 4.1.2.56     
Accepted name: 2-amino-4,5-dihydroxy-6-oxo-7-(phosphooxy)heptanoate synthase
Reaction: 2-amino-4,5-dihydroxy-6-oxo-7-(phosphooxy)heptanoate = glycerone phosphate + L-aspartate 4-semialdehyde
Other name(s): griI (gene name)
Systematic name: 2-amino-4,5-dihydroxy-6-oxo-7-(phosphooxy)heptanoate L-aspartate 4-semialdehyde-lyase (glycerone phosphate-forming)
Comments: Part of the pathway for the biosynthesis of grixazone, a mixture of yellow pigments produced by the bacterium Streptomyces griseus.
References:
1.  Suzuki, H., Ohnishi, Y., Furusho, Y., Sakuda, S. and Horinouchi, S. Novel benzene ring biosynthesis from C3 and C4 primary metabolites by two enzymes. J. Biol. Chem. 281 (2006) 36944–36951. [PMID: 17003031]
[EC 4.1.2.56 created 2014]
 
 
EC 4.1.2.57     
Accepted name: sulfofructosephosphate aldolase
Reaction: 6-deoxy-6-sulfo-D-fructose 1-phosphate = glycerone phosphate + 2-hydroxy-3-oxopropane-1-sulfonate
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
2-hydroxy-3-oxopropane-1-sulfonate = 3-sulfolactaldehyde
Other name(s): yihT (gene name)
Systematic name: 6-deoxy-6-sulfofructose-1-phosphate 2-hydroxy-3-oxopropane-1-sulfonate-lyase (glycerone-phosphate-forming)
Comments: The enzyme, characterized from the bacterium Escherichia coli, is involved in the degradation pathway of sulfoquinovose, the polar headgroup of sulfolipids found in the photosynthetic membranes of all higher plants, mosses, ferns, algae, and most photosynthetic bacteria, as well as the surface layer of some archaea.
References:
1.  Denger, K., Weiss, M., Felux, A.K., Schneider, A., Mayer, C., Spiteller, D., Huhn, T., Cook, A.M. and Schleheck, D. Sulphoglycolysis in Escherichia coli K-12 closes a gap in the biogeochemical sulphur cycle. Nature 507 (2014) 114–117. [PMID: 24463506]
[EC 4.1.2.57 created 2014]
 
 
EC 4.1.2.58     
Accepted name: 2-dehydro-3,6-dideoxy-6-sulfogluconate aldolase
Reaction: 2-dehydro-3,6-dideoxy-6-sulfo-D-gluconate = (2S)-3-sulfolactaldehyde + pyruvate
Other name(s): KDSG aldolase
Systematic name: 2-dehydro-3,6-dideoxy-6-sulfo-D-gluconate (2S)-3-sulfolactaldehyde-lyase (pyruvate-forming)
Comments: The enzyme, characterized from the bacterium Pseudomonas putida SQ1, participates in a sulfoquinovose degradation pathway.
References:
1.  Felux, A.K., Spiteller, D., Klebensberger, J. and Schleheck, D. Entner-Doudoroff pathway for sulfoquinovose degradation in Pseudomonas putida SQ1. Proc. Natl. Acad. Sci. USA 112 (2015) E4298–E4305. [PMID: 26195800]
[EC 4.1.2.58 created 2016]
 
 
EC 4.1.2.59     
Accepted name: dihydroneopterin phosphate aldolase
Reaction: 7,8-dihydroneopterin 3′-phosphate = 6-(hydroxymethyl)-7,8-dihydropterin + glycolaldehyde phosphate
Other name(s): H2NMP aldolase
Systematic name: 7,8-dihydroneopterin 3′-phosphate glycolaldehyde phosphate-lyase [6-(hydroxymethyl)-7,8-dihydropterin-forming]
Comments: The enzyme participates in methanopterin biosynthesis the archaeon Pyrococcus furiosus. The enzyme is specific for 7,8-dihydroneopterin 3′-phosphate. cf. EC 4.1.2.25, dihydroneopterin aldolase and EC 4.1.2.60, dihydroneopterin triphosphate aldolase.
References:
1.  de Crecy-Lagard, V., Phillips, G., Grochowski, L.L., El Yacoubi, B., Jenney, F., Adams, M.W., Murzin, A.G. and White, R.H. Comparative genomics guided discovery of two missing archaeal enzyme families involved in the biosynthesis of the pterin moiety of tetrahydromethanopterin and tetrahydrofolate. ACS Chem. Biol. 7 (2012) 1807–1816. [PMID: 22931285]
[EC 4.1.2.59 created 2017]
 
 
EC 4.1.2.60     
Accepted name: dihydroneopterin triphosphate aldolase
Reaction: 7,8-dihydroneopterin 3′-triphosphate = 6-(hydroxymethyl)-7,8-dihydropterin + glycolaldehyde triphosphate
Other name(s): PTPS-III
Systematic name: 7,8-dihydroneopterin 3′-triphosphate glycolaldehyde phosphate-lyase [6-(hydroxymethyl)-7,8-dihydropterin-forming]
Comments: The enzyme, which participates in a pathway for folate biosynthesis, is found in the Stramenopiles, a large group that includes oomycetes, various microalgae and brown algae, as well as in several bacterial phyla. It provides a bypass mechanism compensating for the lack of EC 4.1.2.25, dihydroneopterin aldolase. In the malaria parasite Plasmodium falciparum the enzyme is bifunctional and also catalyses the activity of EC 4.2.3.12, 6-pyruvoyltetrahydropterin synthase. cf. EC 4.1.2.59, dihydroneopterin phosphate aldolase.
References:
1.  Dittrich, S., Mitchell, S.L., Blagborough, A.M., Wang, Q., Wang, P., Sims, P.F. and Hyde, J.E. An atypical orthologue of 6-pyruvoyltetrahydropterin synthase can provide the missing link in the folate biosynthesis pathway of malaria parasites. Mol. Microbiol. 67 (2008) 609–618. [PMID: 18093090]
2.  Hyde, J.E., Dittrich, S., Wang, P., Sims, P.F., de Crecy-Lagard, V. and Hanson, A.D. Plasmodium falciparum: a paradigm for alternative folate biosynthesis in diverse microorganisms. Trends Parasitol. 24 (2008) 502–508. [PMID: 18805734]
3.  Pribat, A., Jeanguenin, L., Lara-Nunez, A., Ziemak, M.J., Hyde, J.E., de Crecy-Lagard, V. and Hanson, A.D. 6-pyruvoyltetrahydropterin synthase paralogs replace the folate synthesis enzyme dihydroneopterin aldolase in diverse bacteria. J. Bacteriol. 191 (2009) 4158–4165. [PMID: 19395485]
[EC 4.1.2.60 created 2017]
 
 
EC 4.1.2.61     
Accepted name: feruloyl-CoA hydratase/lyase
Reaction: feruloyl-CoA + H2O = vanillin + acetyl-CoA (overall reaction)
(1a) feruloyl-CoA + H2O = 3-hydroxy-3-(4-hydroxy-3-methoxyphenyl)propanoyl-CoA
(1b) 3-hydroxy-3-(4-hydroxy-3-methoxyphenyl)propanoyl-CoA = vanillin + acetyl-CoA
Other name(s): hydroxycinnamoyl-CoA hydratase lyase; enoyl-CoA hydratase/aldolase; HCHL; ferB (gene name); couA (gene name)
Systematic name: feruloyl-CoA hydro-lyase/vanillin-lyase (acetyl-CoA-forming)
Comments: The enzyme is a member of the enoyl-CoA hydratase/isomerase superfamily. It catalyses a two-step process involving first the hydration of the double bond of feruloyl-CoA and then the cleavage of the resultant β-hydroxy thioester by retro-aldol reaction. (E)-caffeoyl-CoA and (E)-4-coumaroyl-CoA are also substrates.
References:
1.  Pometto, A.L. and Crawford, D.L. Whole-cell bioconversion of vanillin to vanillic acid by Streptomyces viridosporus. Appl. Environ. Microbiol. 45 (1983) 1582–1585. [PMID: 6870241]
2.  Narbad, A. and Gasson, M.J. Metabolism of ferulic acid via vanillin using a novel CoA-dependent pathway in a newly-isolated strain of Pseudomonas fluorescens. Microbiology 144 (1998) 1397–1405. [PMID: 9611814]
3.  Gasson, M.J., Kitamura, Y., McLauchlan, W.R., Narbad, A., Parr, A.J., Parsons, E.L., Payne, J., Rhodes, M.J. and Walton, N.J. Metabolism of ferulic acid to vanillin. A bacterial gene of the enoyl-SCoA hydratase/isomerase superfamily encodes an enzyme for the hydration and cleavage of a hydroxycinnamic acid SCoA thioester. J. Biol. Chem. 273 (1998) 4163–4170. [PMID: 9461612]
4.  Overhage, J., Priefert, H. and Steinbuchel, A. Biochemical and genetic analyses of ferulic acid catabolism in Pseudomonas sp. Strain HR199. Appl. Environ. Microbiol. 65 (1999) 4837–4847. [PMID: 10543794]
5.  Bennett, J.P., Bertin, L., Moulton, B., Fairlamb, I.J., Brzozowski, A.M., Walton, N.J. and Grogan, G. A ternary complex of hydroxycinnamoyl-CoA hydratase-lyase (HCHL) with acetyl-CoA and vanillin gives insights into substrate specificity and mechanism. Biochem. J. 414 (2008) 281–289. [PMID: 18479250]
6.  Hirakawa, H., Schaefer, A.L., Greenberg, E.P. and Harwood, C.S. Anaerobic p-coumarate degradation by Rhodopseudomonas palustris and identification of CouR, a MarR repressor protein that binds p-coumaroyl coenzyme A. J. Bacteriol. 194 (2012) 1960–1967. [PMID: 22328668]
7.  Yang, W., Tang, H., Ni, J., Wu, Q., Hua, D., Tao, F. and Xu, P. Characterization of two Streptomyces enzymes that convert ferulic acid to vanillin. PLoS One 8:e67339 (2013). [PMID: 23840666]
[EC 4.1.2.61 created 2020 (EC 4.1.2.41 created 2000, incorporated 2020, EC 4.2.1.101 created 2000, incorporated 2020)]
 
 
EC 4.1.2.62     
Accepted name: 5-deoxyribulose 1-phosphate aldolase
Reaction: (1) 5-deoxy-D-ribulose 1-phosphate = glycerone phosphate + acetaldehyde
(2) S-methyl-5-thio-D-ribulose 1-phosphate = glycerone phosphate + (2-methylsulfanyl)acetaldehyde
Other name(s): 5-(methylthio)ribulose-1-phosphate aldolase; ald2 (gene name)
Systematic name: 5-deoxy-D-ribulose 1-phosphate acetaldehyde-lyase (glycerone-phosphate-forming)
Comments: The enzyme, originally characterized from the bacterium Rhodospirillum rubrum, is involved in degradation pathways for 5′-deoxyadenosine and S-methyl-5′-thioadenosine, which are formed from S-adenosyl-L-methionine (SAM, AdoMet) by radical SAM enzymes and other types of SAM-dependent enzymes, respectively. The enzyme requires a divalent metal cation, with Co2+ producing the highest activity.
References:
1.  North, J.A., Miller, A.R., Wildenthal, J.A., Young, S.J. and Tabita, F.R. Microbial pathway for anaerobic 5′-methylthioadenosine metabolism coupled to ethylene formation. Proc. Natl. Acad. Sci. USA 114 (2017) E10455–E10464. [PMID: 29133429]
2.  North, J.A., Wildenthal, J.A., Erb, T.J., Evans, B.S., Byerly, K.M., Gerlt, J.A. and Tabita, F.R. A bifunctional salvage pathway for two distinct S-adenosylmethionine by-products that is widespread in bacteria, including pathogenic Escherichia coli. Mol. Microbiol. (2020) . [PMID: 31950558]
[EC 4.1.2.62 created 2020]
 
 
EC 4.1.3.1     
Accepted name: isocitrate lyase
Reaction: isocitrate = succinate + glyoxylate
Glossary: isocitrate = (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate (previously known as threo-Ds-isocitrate)
Other name(s): isocitrase; isocitritase; isocitratase; threo-Ds-isocitrate glyoxylate-lyase; isocitrate glyoxylate-lyase
Systematic name: isocitrate glyoxylate-lyase (succinate-forming)
Comments: The isomer of isocitrate involved is (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate [3].
References:
1.  McFadden, B.A. and Howes, W.V. Crystallisation and some properties of isocitrate lyase from Pseudomonas indigofera. J. Biol. Chem. 238 (1963) 1737–1742.
2.  Shiio, I., Shiio, T. and McFadden, B.A. Isocitrate lyase from Pseudomonas indigofera. I. Preparation, amino acid composition and molecular weight. Biochim. Biophys. Acta 96 (1965) 114–122. [PMID: 14285253]
3.  Vickery, H.B. A suggested new nomenclature for the isomers of isocitric acid. J. Biol. Chem. 237 (1962) 1739–1741. [PMID: 13925783]
[EC 4.1.3.1 created 1961]
 
 
EC 4.1.3.2      
Transferred entry: malate synthase. Now EC 2.3.3.9, malate synthase
[EC 4.1.3.2 created 1961, deleted 2002]
 
 
EC 4.1.3.3     
Accepted name: N-acetylneuraminate lyase
Reaction: N-acetylneuraminate = N-acetyl-D-mannosamine + pyruvate
Other name(s): N-acetylneuraminic acid aldolase; acetylneuraminate lyase; sialic aldolase; sialic acid aldolase; sialate lyase; N-acetylneuraminic aldolase; neuraminic aldolase; N-acetylneuraminate aldolase; neuraminic acid aldolase; N-acetylneuraminic acid aldolase; neuraminate aldolase; N-acetylneuraminic lyase; N-acetylneuraminic acid lyase; NPL; NALase; NANA lyase; acetylneuraminate pyruvate-lyase; N-acetylneuraminate pyruvate-lyase
Systematic name: N-acetylneuraminate pyruvate-lyase (N-acetyl-D-mannosamine-forming)
Comments: Also acts on N-glycoloylneuraminate, and on O-acetylated sialic acids, other than 4-O-acetylated derivatives.
References:
1.  Comb, D.G. and Roseman, S. The sialic acids. I. The structure and enzymatic synthesis of N-acetylneuraminic acid. J. Biol. Chem. 235 (1960) 2529–2537. [PMID: 13811398]
2.  Schauer, R. Sialic acids. Adv. Carbohydr. Chem. Biochem. 40 (1982) 131–234. [PMID: 6762816]
[EC 4.1.3.3 created 1961]
 
 
EC 4.1.3.4     
Accepted name: hydroxymethylglutaryl-CoA lyase
Reaction: (S)-3-hydroxy-3-methylglutaryl-CoA = acetyl-CoA + acetoacetate
Other name(s): hydroxymethylglutaryl coenzyme A-cleaving enzyme; hydroxymethylglutaryl coenzyme A lyase; 3-hydroxy-3-methylglutaryl coenzyme A lyase; 3-hydroxy-3-methylglutaryl CoA cleaving enzyme; 3-hydroxy-3-methylglutaryl-CoA lyase; (S)-3-hydroxy-3-methylglutaryl-CoA acetoacetate-lyase
Systematic name: (S)-3-hydroxy-3-methylglutaryl-CoA acetoacetate-lyase (acetyl-CoA-forming)
References:
1.  Bachhawat, B.K., Robinson, W.G. and Coon, M.J. The enzymatic cleavage of β-hydroxy-β-methylglutaryl coenzyme A to acetoacetate and acetyl coenzyme A. J. Biol. Chem. 216 (1955) 727–736. [PMID: 13271348]
[EC 4.1.3.4 created 1961]
 
 
EC 4.1.3.5      
Transferred entry: hydroxymethylglutaryl-CoA synthase. Now EC 2.3.3.10, hydroxymethylglutaryl-CoA synthase
[EC 4.1.3.5 created 1961, deleted 2002]
 
 
EC 4.1.3.6     
Accepted name: citrate (pro-3S)-lyase
Reaction: citrate = acetate + oxaloacetate
Other name(s): citrase; citratase; citritase; citridesmolase; citrate aldolase; citric aldolase; citrate lyase; citrate oxaloacetate-lyase; citrate oxaloacetate-lyase [(pro-3S)-CH2COO-→acetate]
Systematic name: citrate oxaloacetate-lyase (forming acetate from the pro-S carboxymethyl group of citrate)
Comments: The enzyme can be dissociated into components, two of which are identical with EC 2.8.3.10 (citrate CoA-transferase) and EC 4.1.3.34 (citryl-CoA lyase). EC 3.1.2.16, citrate lyase deacetylase, deacetylates and inactivates the enzyme.
References:
1.  Dagley, S. and Dawes, E.A. Citridesmolase: its properties and mode of action. Biochim. Biophys. Acta 17 (1955) 177–184. [PMID: 13239657]
2.  Dimroth, P., Loyal, R. and Eggerer, H. Characterization of the isolated transferase subunit of citrate lyase as a CoA-transferase. Evidence against a covalent enzyme-substrate intermediate. Eur. J. Biochem. 80 (1977) 479–488. [PMID: 336371]
[EC 4.1.3.6 created 1961]
 
 
EC 4.1.3.7      
Transferred entry: citrate (Si)-synthase. Now EC 2.3.3.1, citrate (Si)-synthase
[EC 4.1.3.7 created 1961, deleted 2002]
 
 
EC 4.1.3.8      
Transferred entry: ATP citrate (pro-S)-lyase. Now EC 2.3.3.8, ATP citrate synthase
[EC 4.1.3.8 created 1965, modified 1986, deleted 2002]
 
 
EC 4.1.3.9      
Transferred entry: 2-hydroxyglutarate synthase. Now EC 2.3.3.11, 2-hydroxyglutarate synthase
[EC 4.1.3.9 created 1965, deleted 2002]
 
 
EC 4.1.3.10      
Transferred entry: 3-ethylmalate synthase. Now EC 2.3.3.7, 3-ethylmalate synthase
[EC 4.1.3.10 created 1965, modified 1983, deleted 2002]
 
 
EC 4.1.3.11      
Transferred entry: 3-propylmalate synthase. Now EC 2.3.3.12, 3-propylmalate synthase
[EC 4.1.3.11 created 1972, deleted 2002]
 
 
EC 4.1.3.12      
Transferred entry: 2-isopropylmalate synthase. Now EC 2.3.3.13, 2-isopropylmalate synthase
[EC 4.1.3.12 created 1972, deleted 2002]
 
 
EC 4.1.3.13     
Accepted name: oxalomalate lyase
Reaction: 3-oxalomalate = oxaloacetate + glyoxylate
Other name(s): 3-oxalomalate glyoxylate-lyase
Systematic name: 3-oxalomalate glyoxylate-lyase (oxaloacetate-forming)
References:
1.  Sekizawa, Y., Maragoudakis, M.E., King, T.E. and Cheldelin, V.H. Glutamate biosynthesis in an organism lacking a Krebs tricarboxylic acid cycle. V. Isolation of α-hydroxy-γ-ketoglutarate (HKG) in Acetobacter suboxydans. Biochemistry 5 (1966) 2392–2398. [PMID: 6005666]
[EC 4.1.3.13 created 1972]
 
 
EC 4.1.3.14     
Accepted name: L-erythro-3-hydroxyaspartate aldolase
Reaction: L-erythro-3-hydroxy-aspartate = glycine + glyoxylate
Other name(s): L-erythro-β-hydroxyaspartate aldolase; L-erythro-β-hydroxyaspartate glycine-lyase; erythro-3-hydroxy-Ls-aspartate glyoxylate-lyase
Systematic name: L-erythro-3-hydroxy-aspartate glyoxylate-lyase (glycine-forming)
Comments: A pyridoxal-phosphate protein. The enzyme, purified from the bacterium Paracoccus denitrificans NCIMB 8944, is strictly specific for the L-erythro stereoisomer of 3-hydroxyaspartate. Different from EC 4.1.3.41, erythro-3-hydroxy-D-aspartate aldolase. Requires a divalent cation.
References:
1.  Gibbs, R.G. and Morris, J.G. Assay and properties of β-hydroxyaspartate aldolase from Micrococcus denitrificans. Biochim. Biophys. Acta 85 (1964) 501–503. [PMID: 14194868]
[EC 4.1.3.14 created 1972, modified 2011]
 
 
EC 4.1.3.15      
Transferred entry: 2-hydroxy-3-oxoadipate synthase. Now EC 2.2.1.5, 2-hydroxy-3-oxoadipate synthase
[EC 4.1.3.15 created 1972, deleted 2002]
 
 
EC 4.1.3.16     
Accepted name: 4-hydroxy-2-oxoglutarate aldolase
Reaction: 4-hydroxy-2-oxoglutarate = pyruvate + glyoxylate
Other name(s): 2-oxo-4-hydroxyglutarate aldolase; hydroxyketoglutaric aldolase; 4-hydroxy-2-ketoglutaric aldolase; 2-keto-4-hydroxyglutaric aldolase; 4-hydroxy-2-ketoglutarate aldolase; 2-keto-4-hydroxyglutarate aldolase; 2-oxo-4-hydroxyglutaric aldolase; DL-4-hydroxy-2-ketoglutarate aldolase; hydroxyketoglutarate aldolase; 2-keto-4-hydroxybutyrate aldolase; 4-hydroxy-2-oxoglutarate glyoxylate-lyase; KHGA
Systematic name: 4-hydroxy-2-oxoglutarate glyoxylate-lyase (pyruvate-forming)
Comments: The enzymes from rat liver and bovine liver act on both enantiomers of 4-hydroxy-2-oxoglutarate. cf. EC 4.1.3.42, (4S)-4-hydroxy-2-oxoglutarate aldolase.
References:
1.  Kuratomi, K. and Fukunaga, K. The metabolism of γ-hydroxyglutamate in rat liver. I. Enzymic synthesis of γ-hydroxy-α-ketoglutarate from pyruvate and glyoxalate. Biochim. Biophys. Acta 78 (1963) 617–628. [PMID: 14089442]
2.  Kobes, R.D. and Dekker, E.E. 2-Keto-4-hydroxyglutarate aldolase of bovine liver. Purification, criteria of purity, and general properties. J. Biol. Chem. 244 (1969) 1919–1925. [PMID: 5780845]
3.  Lane, R.S., Shapley, A. and Dekker, E.E. 2-keto-4-hydroxybutyrate aldolase. Identification as 2-keto-4-hydroxyglutarate aldolase, catalytic properties, and role in the mammalian metabolism of L-homoserine. Biochemistry 10 (1971) 1353–1364. [PMID: 5580656]
4.  Scholtz, J.M. and Schuster, S.M. Regulation of rat liver 4-hydroxy-2-ketoglutarate aldolase. Biochim. Biophys. Acta 869 (1986) 192–196. [PMID: 3942759]
[EC 4.1.3.16 created 1972 (EC 4.1.2.1 created 1961, incorporated 1972, EC 4.1.2.31 created 1978, incorporated 1982)]
 
 
EC 4.1.3.17     
Accepted name: 4-hydroxy-4-methyl-2-oxoglutarate aldolase
Reaction: (1) 4-hydroxy-4-methyl-2-oxoglutarate = 2 pyruvate
(2) 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate = oxaloacetate + pyruvate
Other name(s): pyruvate aldolase; γ-methyl-γ-hydroxy-α-ketoglutaric aldolase; 4-hydroxy-4-methyl-2-ketoglutarate aldolase; 4-hydroxy-4-methyl-2-oxoglutarate pyruvate-lyase; HMG aldolase; CHA aldolase; 4-carboxy-4-hydroxy-2-oxoadipate aldolase
Systematic name: 4-hydroxy-4-methyl-2-oxoglutarate pyruvate-lyase (pyruvate-forming)
Comments: Requires a divalent metal ion [3]. This enzyme participates in the degradation of 3,4-dihydroxybenzoate (via the meta-cleavage pathway), phthalate, syringate and 3,4,5-trihydroxybenzoate [1-3]. The enzyme from Pseudomonas straminea can also catalyse the activity of EC 4.1.3.16, 4-hydroxy-2-oxoglutarate aldolase, and the decarboxylation of oxaloacetate [3].
References:
1.  Tack, B.F., Chapman, P.J. and Dagley, S. Purification and properties of 4-hydroxy-4-methyl-2-oxoglutarate aldolase. J. Biol. Chem. 247 (1972) 6444–6449. [PMID: 5076765]
2.  Wood, W.A. 2-Keto-3-deoxy-6-phosphogluconic and related aldolases. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 7, Academic Press, New York, 1972, pp. 281–302.
3.  Maruyama, K. Purification and properties of 4-hydroxy-4-methyl-2-oxoglutarate aldolase from Pseudomonas ochraceae grown on phthalate. J. Biochem. 108 (1990) 327–333. [PMID: 2229032]
4.  Nogales, J., Canales, A., Jiménez-Barbero, J., Serra B., Pingarrón, J. M., García, J. L. and Díaz, E. Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida. Mol. Microbiol. 79 (2011) 359–374. [PMID: 21219457]
[EC 4.1.3.17 created 1972, modified 2012]
 
 
EC 4.1.3.18      
Transferred entry: acetolactate synthase. Now EC 2.2.1.6, acetolactate synthase
[EC 4.1.3.18 created 1972, deleted 2002]
 
 
EC 4.1.3.19      
Transferred entry: N-acetylneuraminate synthase. Now EC 2.5.1.56, N-acetylneuraminate synthase
[EC 4.1.3.19 created 1972, deleted 2002]
 
 
EC 4.1.3.20      
Transferred entry: N-acylneuraminate-9-phosphate synthase. Now EC 2.5.1.57, N-acylneuraminate-9-phosphate synthase
[EC 4.1.3.20 created 1972, deleted 2002]
 
 
EC 4.1.3.21      
Transferred entry: homocitrate synthase. Now EC 2.3.3.14, homocitrate synthase
[EC 4.1.3.21 created 1972, deleted 2002]
 
 
EC 4.1.3.22     
Accepted name: citramalate lyase
Reaction: (2S)-2-hydroxy-2-methylbutanedioate = acetate + pyruvate
Glossary: (+)-citramalate = (2S)-2-hydroxy-2-methylbutanedioate
Other name(s): citramalate pyruvate-lyase; citramalate synthase; citramalic-condensing enzyme; citramalate synthetase; citramalic synthase; (S)-citramalate lyase; (+)-citramalate pyruvate-lyase; citramalate pyruvate lyase; (3S)-citramalate pyruvate-lyase; (2S)-2-hydroxy-2-methylbutanedioate pyruvate-lyase
Systematic name: (2S)-2-hydroxy-2-methylbutanedioate pyruvate-lyase (acetate-forming)
Comments: The enzyme can be dissociated into components, two of which are identical with EC 2.8.3.11 (citramalate CoA-transferase) and EC 4.1.3.25 (citramalyl-CoA lyase).
References:
1.  Barker, H.A. Citramalate lyase of Clostridium tetanomorphum. Arch. Mikrobiol. 59 (1967) 4–12. [PMID: 4301387]
2.  Dimroth, P., Buckel, W., Loyal, R. and Eggerer, H. Isolation and function of the subunits of citramalate lyase and formation of hybrids with the subunits of citrate lyase. Eur. J. Biochem. 80 (1977) 469–477. [PMID: 923590]
[EC 4.1.3.22 created 1972]
 
 
EC 4.1.3.23      
Transferred entry: decylcitrate synthase. Now EC 2.3.3.2, decylcitrate synthase
[EC 4.1.3.23 created 1972, deleted 2002]
 
 
EC 4.1.3.24     
Accepted name: malyl-CoA lyase
Reaction: (1) (S)-malyl-CoA = acetyl-CoA + glyoxylate
(2) (2R,3S)-2-methylmalyl-CoA = propanoyl-CoA + glyoxylate
Glossary: (S)-malyl-CoA = (3S)-3-carboxy-3-hydroxypropanoyl-CoA
(2R,3S)-2-methylmalyl-CoA = L-erythro-β-methylmalyl-CoA = (2R,3S)-2-methyl-3-carboxy-3-hydroxypropanoyl-CoA
Other name(s): malyl-coenzyme A lyase; (3S)-3-carboxy-3-hydroxypropanoyl-CoA glyoxylate-lyase; mclA (gene name); mcl1 (gene name); (3S)-3-carboxy-3-hydroxypropanoyl-CoA glyoxylate-lyase (acetyl-CoA-forming); L-malyl-CoA lyase
Systematic name: (S)-malyl-CoA glyoxylate-lyase (acetyl-CoA-forming)
Comments: The enzymes from Rhodobacter species catalyse a step in the ethylmalonyl-CoA pathway for acetate assimilation [3,5]. The enzyme from halophilic bacteria participate in the methylaspartate cycle and catalyse the reaction in the direction of malyl-CoA formation [6]. The enzyme from the bacterium Chloroflexus aurantiacus, which participates in the 3-hydroxypropanoate cycle for carbon assimilation, also has the activity of EC 4.1.3.25, (3S)-citramalyl-CoA lyase [2,4].
References:
1.  Tuboi, S. and Kikuchi, G. Enzymic cleavage of malyl-Coenzyme A into acetyl-Coenzyme A and glyoxylic acid. Biochim. Biophys. Acta 96 (1965) 148–153. [PMID: 14285256]
2.  Herter, S., Busch, A. and Fuchs, G. L-Malyl-coenzyme A lyase/β-methylmalyl-coenzyme A lyase from Chloroflexus aurantiacus, a bifunctional enzyme involved in autotrophic CO2 fixation. J. Bacteriol. 184 (2002) 5999–6006. [PMID: 12374834]
3.  Meister, M., Saum, S., Alber, B.E. and Fuchs, G. L-Malyl-coenzyme A/β-methylmalyl-coenzyme A lyase is involved in acetate assimilation of the isocitrate lyase-negative bacterium Rhodobacter capsulatus. J. Bacteriol. 187 (2005) 1415–1425. [PMID: 15687206]
4.  Friedmann, S., Alber, B.E. and Fuchs, G. Properties of R-citramalyl-coenzyme A lyase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus. J. Bacteriol. 189 (2007) 2906–2914. [PMID: 17259315]
5.  Erb, T.J., Frerichs-Revermann, L., Fuchs, G. and Alber, B.E. The apparent malate synthase activity of Rhodobacter sphaeroides is due to two paralogous enzymes, (3S)-malyl-coenzyme A (CoA)/β-methylmalyl-CoA lyase and (3S)-malyl-CoA thioesterase. J. Bacteriol. 192 (2010) 1249–1258. [PMID: 20047909]
6.  Borjian, F., Han, J., Hou, J., Xiang, H., Zarzycki, J. and Berg, I.A. Malate Synthase and β-Methylmalyl Coenzyme A Lyase Reactions in the Methylaspartate Cycle in Haloarcula hispanica. J. Bacteriol. 199 (2017) . [PMID: 27920298]
[EC 4.1.3.24 created 1972, modified 2014]
 
 
EC 4.1.3.25     
Accepted name: (S)-citramalyl-CoA lyase
Reaction: (3S)-citramalyl-CoA = acetyl-CoA + pyruvate
Other name(s): citramalyl coenzyme A lyase (ambiguous); (+)-CMA-CoA lyase; (3S)-citramalyl-CoA pyruvate-lyase; Mcl (ambiguous); citramalyl-CoA lyase (ambiguous)
Systematic name: (3S)-citramalyl-CoA pyruvate-lyase (acetyl-CoA-forming)
Comments: Requires Mg2+ ions for activity [3]. The enzyme from the bacterium Clostridium tetanomorphum is a component of EC 4.1.3.22, citramalate lyase [2]. It also acts on (3S)-citramalyl thioacyl-carrier protein [2]. The enzyme from the bacterium Chloroflexus aurantiacus also has the activity of EC 4.1.3.24, malyl-CoA lyase [3]. It has no activity with (3R)-citramalyl-CoA (cf. EC 4.1.3.46, (R)-citramalyl-CoA lyase) [3].
References:
1.  Cooper, R.A. and Kornberg, H.L. The utilization of itaconate by Pseudomonas sp. Biochem. J. 91 (1964) 82–91. [PMID: 4284209]
2.  Dimroth, P., Buckel, W., Loyal, R. and Eggerer, H. Isolation and function of the subunits of citramalate lyase and formation of hybrids with the subunits of citrate lyase. Eur. J. Biochem. 80 (1977) 469–477. [PMID: 923590]
3.  Friedmann, S., Alber, B.E. and Fuchs, G. Properties of R-citramalyl-coenzyme A lyase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus. J. Bacteriol. 189 (2007) 2906–2914. [PMID: 17259315]
[EC 4.1.3.25 created 1972, modified 2014]
 
 
EC 4.1.3.26     
Accepted name: 3-hydroxy-3-isohexenylglutaryl-CoA lyase
Reaction: 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA = 7-methyl-3-oxooct-6-enoyl-CoA + acetate
Other name(s): β-hydroxy-β-isohexenylglutaryl CoA-lyase; hydroxyisohexenylglutaryl-CoA:acetatelyase; 3-hydroxy-3-isohexenylglutaryl coenzyme A lyase; 3-hydroxy-3-isohexenylglutaryl-CoA isopentenylacetoacetyl-CoA-lyase; 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA acetate-lyase
Systematic name: 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA acetate-lyase (7-methyl-3-oxooct-6-enoyl-CoA-forming)
Comments: Also acts on the hydroxy derivative of farnesoyl-CoA.
References:
1.  Seubert, W. and Fass, E. Untersuchungen über den bakterielle Abbau von Isoprenoiden. IV. Reinigung und Eigenschaftender β-Isohexenylglutaconyl-CoA-hydratase und β-Hydroxy-β-isohexenylglutaryl-CoA-lyase. Biochem. Z. 341 (1964) 23–34. [PMID: 14339651]
[EC 4.1.3.26 created 1972]
 
 
EC 4.1.3.27     
Accepted name: anthranilate synthase
Reaction: chorismate + L-glutamine = anthranilate + pyruvate + L-glutamate
Other name(s): anthranilate synthetase; chorismate lyase; chorismate pyruvate-lyase (amino-accepting); TrpE
Systematic name: chorismate pyruvate-lyase (amino-accepting; anthranilate-forming)
Comments: In some organisms, this enzyme is part of a multifunctional protein, together with one or more other components of the system for the biosynthesis of tryptophan [EC 2.4.2.18 (anthranilate phosphoribosyltransferase ), EC 4.1.1.48 (indole-3-glycerol-phosphate synthase), EC 4.2.1.20 (tryptophan synthase) and EC 5.3.1.24 (phosphoribosylanthranilate isomerase)]. The native enzyme in the complex uses either glutamine or, less efficiently, NH3. The enzyme separated from the complex uses NH3 only.
References:
1.  Baker, T. and Crawford, I.P. Anthranilate synthetase. Partial purification and some kinetic studies on the enzyme from Escherichia coli. J. Biol. Chem. 241 (1966) 5577–5584. [PMID: 5333199]
2.  Creighton, T.E. and Yanofsky, C. Chorismate to tryptophan (Escherichia coli) - anthranilate synthetase, PR transferase, PRA isomerase, InGP synthetase, tryptophan synthetase. Methods Enzymol. 17A (1970) 365–380.
3.  Hütter, R., Niederberger, P. and DeMoss, J.A. Tryptophan synthetic genes in eukaryotic microorganisms. Annu. Rev. Microbiol. 40 (1986) 55–77. [PMID: 3535653]
4.  Ito, J. and Yanofsky, C. Anthranilate synthetase, an enzyme specified by the tryptophan operon of Escherichia coli: Comparative studies on the complex and the subunits. J. Bacteriol. 97 (1969) 734–742. [PMID: 4886290]
5.  Zalkin, H. and Kling, D. Anthranilate synthetase. Purification and properties of component I from Salmonella typhimurium. Biochemistry 7 (1968) 3566–3573. [PMID: 4878701]
[EC 4.1.3.27 created 1972]
 
 
EC 4.1.3.28      
Transferred entry: citrate (Re)-synthase. Now EC 2.3.3.3, citrate (Re)-synthase
[EC 4.1.3.28 created 1972, deleted 2002]
 
 
EC 4.1.3.29      
Transferred entry: decylhomocitrate synthase. Now EC 2.3.3.4, decylhomocitrate synthase
[EC 4.1.3.29 created 1976, deleted 2002]
 
 
EC 4.1.3.30     
Accepted name: methylisocitrate lyase
Reaction: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = succinate + pyruvate
Glossary: (2S,3R)-2-methylisocitrate = (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = threo-Ds-2-methylisocitrate
Other name(s): 2-methylisocitrate lyase; MICL; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate pyruvate-lyase
Systematic name: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate pyruvate-lyase (succinate-forming)
Comments: The enzyme acts on threo-Ds-2-methylisocitrate, but not on threo-Ds-isocitrate, threo-DL-isocitrate or erythro-Ls-isocitrate.
References:
1.  Tabuchi, T. and Satoh, T. Distinction between isocitrate lyase and methylisocitrate lyase in Candida lipolytica. Agric. Biol. Chem. 40 (1976) 1863–1869.
2.  Tabuchi, T. and Satoh, T. Purification and properties of methylisocitrate lyase, a key enzyme in propionate metabolism, from Candida lipolytica. Agric. Biol. Chem. 41 (1977) 169–174.
[EC 4.1.3.30 created 1978]
 
 
EC 4.1.3.31      
Transferred entry: 2-methylcitrate synthase. Now EC 2.3.3.5, 2-methylcitrate synthase
[EC 4.1.3.31 created 1978, deleted 2002]
 
 
EC 4.1.3.32     
Accepted name: 2,3-dimethylmalate lyase
Reaction: (2R,3S)-2,3-dimethylmalate = propanoate + pyruvate
Other name(s): 2,3-dimethylmalate pyruvate-lyase; (2R,3S)-2,3-dimethylmalate pyruvate-lyase
Systematic name: (2R,3S)-2,3-dimethylmalate pyruvate-lyase (propanoate-forming)
References:
1.  Pirzer, P., Lill, U. and Eggerer, H. Nicotinic acid metabolism. 2,3-Dimethylmalate lyase. Hoppe-Seyler's Z. Physiol. Chem. 360 (1979) 1693–1702. [PMID: 527937]
2.  Alhapel, A., Darley, D.J., Wagener, N., Eckel, E., Elsner, N. and Pierik, A.J. Molecular and functional analysis of nicotinate catabolism in Eubacterium barkeri. Proc. Natl. Acad. Sci. USA 103 (2006) 12341–12346. [PMID: 16894175]
[EC 4.1.3.32 created 1981]
 
 
EC 4.1.3.33      
Transferred entry: 2-ethylmalate synthase. Now EC 2.3.3.6, 2-ethylmalate synthase
[EC 4.1.3.33 created 1983, deleted 2002]
 
 
EC 4.1.3.34     
Accepted name: citryl-CoA lyase
Reaction: (3S)-citryl-CoA = acetyl-CoA + oxaloacetate
Other name(s): (3S)-citryl-CoA oxaloacetate-lyase
Systematic name: (3S)-citryl-CoA oxaloacetate-lyase (acetyl-CoA-forming)
Comments: The enzyme is a component of EC 4.1.3.6 {[citrate (pro-3S)-lyase]}and EC 2.3.3.8 [ATP citrate synthase]. Also acts on (3S)-citryl thioacyl-carrier protein.
References:
1.  Dimroth, P., Loyal, R. and Eggerer, H. Characterization of the isolated transferase subunit of citrate lyase as a CoA-transferase. Evidence against a covalent enzyme-substrate intermediate. Eur. J. Biochem. 80 (1977) 479–488. [PMID: 336371]
2.  Lill, U., Schreil, A. and Eggerer, H. Isolation of enzymically active fragments formed by limited proteolysis of ATP citrate lyase. Eur. J. Biochem. 125 (1982) 645–650. [PMID: 6749502]
[EC 4.1.3.34 created 1984, modified 1986]
 
 
EC 4.1.3.35     
Accepted name: (1-hydroxycyclohexan-1-yl)acetyl-CoA lyase
Reaction: (1-hydroxycyclohexan-1-yl)acetyl-CoA = acetyl-CoA + cyclohexanone
Other name(s): (1-hydroxycyclohexan-1-yl)acetyl-CoA cyclohexanone-lyase
Systematic name: (1-hydroxycyclohexan-1-yl)acetyl-CoA cyclohexanone-lyase (acetyl-CoA-forming)
References:
1.  Ougham, H.J. and Trudgill, P.W. Metabolism of cyclohexaneacetic acid and cyclohexanebutyric acid by Arthrobacter sp. strain CA1. J. Bacteriol. 150 (1982) 1172–1182. [PMID: 7076617]
[EC 4.1.3.35 created 1986]
 
 
EC 4.1.3.36     
Accepted name: 1,4-dihydroxy-2-naphthoyl-CoA synthase
Reaction: 4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H2O
Other name(s): naphthoate synthase; 1,4-dihydroxy-2-naphthoate synthase; dihydroxynaphthoate synthase; o-succinylbenzoyl-CoA 1,4-dihydroxy-2-naphthoate-lyase (cyclizing); MenB; o-succinylbenzoyl-CoA dehydratase (cyclizing)
Systematic name: 4-(2-carboxyphenyl)-4-oxobutanoyl-CoA dehydratase (cyclizing)
Comments: This enzyme is involved in the synthesis of 1,4-dihydroxy-2-naphthoate, a branch point metabolite leading to the biosynthesis of menaquinone (vitamin K2, in bacteria), phylloquinone (vitamin K1 in plants), and many plant pigments. The coenzyme A group is subsequently removed from the product by EC 3.1.2.28, 1,4-dihydroxy-2-naphthoyl-CoA hydrolase.
References:
1.  Meganathan, R. and Bentley, R. Menaquinone (vitamin K2) biosynthesis: conversion of o-succinylbenzoic acid to 1,4-dihydroxy-2-naphthoic acid by Mycobacterium phlei enzymes. J. Bacteriol. 140 (1979) 92–98. [PMID: 500558]
2.  Kolkmann, R. and Leistner, E. 4-(2′-Carboxyphenyl)-4-oxobutyryl coenzyme A ester, an intermediate in vitamin K2 (menaquinone) biosynthesis. Z. Naturforsch. C: Sci. 42 (1987) 1207–1214. [PMID: 2966501]
3.  Johnson, T.W., Shen, G., Zybailov, B., Kolling, D., Reategui, R., Beauparlant, S., Vassiliev, I.R., Bryant, D.A., Jones, A.D., Golbeck, J.H. and Chitnis, P.R. Recruitment of a foreign quinone into the A(1) site of photosystem I. I. Genetic and physiological characterization of phylloquinone biosynthetic pathway mutants in Synechocystis sp. PCC 6803. J. Biol. Chem. 275 (2000) 8523–8530. [PMID: 10722690]
4.  Truglio, J.J., Theis, K., Feng, Y., Gajda, R., Machutta, C., Tonge, P.J. and Kisker, C. Crystal structure of Mycobacterium tuberculosis MenB, a key enzyme in vitamin K2 biosynthesis. J. Biol. Chem. 278 (2003) 42352–42360. [PMID: 12909628]
[EC 4.1.3.36 created 1992, modified 2010]
 
 
EC 4.1.3.37      
Transferred entry: 1-deoxy-D-xylulose 5-phosphate synthase. Now EC 2.2.1.7, 1-deoxy-D-xylulose 5-phosphate synthase
[EC 4.1.3.37 created 2001, deleted 2002]
 
 
EC 4.1.3.38     
Accepted name: aminodeoxychorismate lyase
Reaction: 4-amino-4-deoxychorismate = 4-aminobenzoate + pyruvate
Other name(s): enzyme X; 4-amino-4-deoxychorismate lyase; 4-amino-4-deoxychorismate pyruvate-lyase
Systematic name: 4-amino-4-deoxychorismate pyruvate-lyase (4-aminobenzoate-forming)
Comments: A pyridoxal-phosphate protein. Forms part of the folate biosynthesis pathway. Acts on 4-amino-4-deoxychorismate, the product of EC 2.6.1.85, aminodeoxychorismate synthase, to form p-aminobenzoate.
References:
1.  Ye, Q.Z., Liu, J. and Walsh, C.T. p-Aminobenzoate synthesis in Escherichia coli: purification and characterization of PabB as aminodeoxychorismate synthase and enzyme X as aminodeoxychorismate lyase. Proc. Natl. Acad. Sci. USA 87 (1990) 9391–9395. [PMID: 2251281]
2.  Green, J.M., Merkel, W.K. and Nichols, B.P. Characterization and sequence of Escherichia coli pabC, the gene encoding aminodeoxychorismate lyase, a pyridoxal phosphate-containing enzyme. J. Bacteriol. 174 (1992) 5317–5323. [PMID: 1644759]
3.  Nakai, T., Mizutani, H., Miyahara, I., Hirotsu, K., Takeda, S., Jhee, K.H., Yoshimura, T. and Esaki, N. Three-dimensional structure of 4-amino-4-deoxychorismate lyase from Escherichia coli. J. Biochem. 128 (2000) 29–38. [PMID: 10876155]
[EC 4.1.3.38 created 2003]
 
 
EC 4.1.3.39     
Accepted name: 4-hydroxy-2-oxovalerate aldolase
Reaction: (S)-4-hydroxy-2-oxopentanoate = acetaldehyde + pyruvate
Glossary: (S)-4-hydroxy-2-oxopentanoate = (S)-4-hydroxy-2-oxovalerate
Other name(s): 4-hydroxy-2-ketovalerate aldolase; HOA; DmpG; 4-hydroxy-2-oxovalerate pyruvate-lyase; 4-hydroxy-2-oxopentanoate pyruvate-lyase; BphI; 4-hydroxy-2-oxopentanoate pyruvate-lyase (acetaldehyde-forming)
Systematic name: (S)-4-hydroxy-2-oxopentanoate pyruvate-lyase (acetaldehyde-forming)
Comments: Requires Mn2+ for maximal activity [1]. The enzyme from the bacterium Pseudomonas putida is also stimulated by NADH [1]. In some bacterial species the enzyme forms a bifunctional complex with EC 1.2.1.10, acetaldehyde dehydrogenase (acetylating). The enzymes from the bacteria Burkholderia xenovorans and Thermus thermophilus also perform the reaction of EC 4.1.3.43, 4-hydroxy-2-oxohexanoate aldolase [4,5].
References:
1.  Manjasetty, B.A., Powlowski, J. and Vrielink, A. Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate. Proc. Natl. Acad. Sci. USA 100 (2003) 6992–6997. [PMID: 12764229]
2.  Powlowski, J., Sahlman, L. and Shingler, V. Purification and properties of the physically associated meta-cleavage pathway enzymes 4-hydroxy-2-ketovalerate aldolase and aldehyde dehydrogenase (acylating) from Pseudomonas sp. strain CF600. J. Bacteriol. 175 (1993) 377–385. [PMID: 8419288]
3.  Manjasetty, B.A., Croteau, N., Powlowski, J. and Vrielink, A. Crystallization and preliminary X-ray analysis of dmpFG-encoded 4-hydroxy-2-ketovalerate aldolase—aldehyde dehydrogenase (acylating) from Pseudomonas sp. strain CF600. Acta Crystallogr. D Biol. Crystallogr. 57 (2001) 582–585. [PMID: 11264589]
4.  Baker, P., Carere, J. and Seah, S.Y.K. Probing the molecular basis of substrate specificity, stereospecificity, and catalysis in the class II pyruvate aldolase, BphI. Biochemistry 50 (2011) 3559–3569. [PMID: 21425833]
5.  Baker, P., Hillis, C., Carere, J. and Seah, S.Y.K. Protein-protein interactions and substrate channeling in orthologous and chimeric aldolase-dehydrogenase complexes. Biochemistry 51 (2012) 1942–1952. [PMID: 22316175]
6.  Baker, P. and Seah, S.Y.K. Rational design of stereoselectivity in the class II pyruvate aldolase BphI. J. Am. Chem. Soc. 134 (2012) 507–513. [PMID: 22081904]
[EC 4.1.3.39 created 2006, modified 2011]
 
 
EC 4.1.3.40     
Accepted name: chorismate lyase
Reaction: chorismate = 4-hydroxybenzoate + pyruvate
Other name(s): CL; CPL; UbiC
Systematic name: chorismate pyruvate-lyase (4-hydroxybenzoate-forming)
Comments: This enzyme catalyses the first step in the biosynthesis of ubiquinone in Escherichia coli and other Gram-negative bacteria [1]. The yeast Saccharomyces cerevisiae can synthesize ubiquinone from either chorismate or tyrosine [3].
References:
1.  Nichols, B.P. and Green, J.M. Cloning and sequencing of Escherichia coli ubiC and purification of chorismate lyase. J. Bacteriol. 174 (1992) 5309–5316. [PMID: 1644758]
2.  Siebert, M., Severin, K. and Heide, L. Formation of 4-hydroxybenzoate in Escherichia coli: characterization of the ubiC gene and its encoded enzyme chorismate pyruvate-lyase. Microbiology 140 (1994) 897–904. [PMID: 8012607]
3.  Meganathan, R. Ubiquinone biosynthesis in microorganisms. FEMS Microbiol. Lett. 203 (2001) 131–139. [PMID: 11583838]
[EC 4.1.3.40 created 2007]
 
 
EC 4.1.3.41     
Accepted name: 3-hydroxy-D-aspartate aldolase
Reaction: (1) threo-3-hydroxy-D-aspartate = glycine + glyoxylate
(2) D-erythro-3-hydroxyaspartate = glycine + glyoxylate
Other name(s): D-3-hydroxyaspartate aldolase
Systematic name: 3-hydroxy-D-aspartate glyoxylate-lyase (glycine-forming)
Comments: A pyridoxal-phosphate protein. The enzyme, purified from the bacterium Paracoccus denitrificans IFO 13301, is strictly D-specific as to the α-position of the substrate, but accepts both the threo and erythro forms at the β-position. The erythro form is a far better substrate (about 100-fold). The enzyme can also accept D-allothreonine, D-threonine, erythro-3-phenyl-D-serine and threo-3-phenyl-D-serine. Different from EC 4.1.3.14, erythro-3-hydroxy-L-aspartate aldolase. Requires a divalent cation, such as Mg2+, Mn2+ or Co2+.
References:
1.  Liu, J.Q., Dairi, T., Itoh, N., Kataoka, M. and Shimizu, S. A novel enzyme, D-3-hydroxyaspartate aldolase from Paracoccus denitrificans IFO 13301: purification, characterization, and gene cloning. Appl. Microbiol. Biotechnol. 62 (2003) 53–60. [PMID: 12835921]
[EC 4.1.3.41 created 2011]
 
 
EC 4.1.3.42     
Accepted name: (4S)-4-hydroxy-2-oxoglutarate aldolase
Reaction: (4S)-4-hydroxy-2-oxoglutarate = pyruvate + glyoxylate
Glossary: (4S)-4-hydroxy-2-oxoglutatrate = (S)-2-hydroxy-4-oxopentanedioate = L-4-hydroxy-2-oxoglutarate
Other name(s): 2-oxo-4-hydroxyglutarate aldolase (ambiguous); hydroxyketoglutaric aldolase (ambiguous); 4-hydroxy-2-ketoglutaric aldolase (ambiguous); 2-keto-4-hydroxyglutaric aldolase (ambiguous); 4-hydroxy-2-ketoglutarate aldolase (ambiguous); 2-keto-4-hydroxyglutarate aldolase (ambiguous); 2-oxo-4-hydroxyglutaric aldolase (ambiguous); hydroxyketoglutarate aldolase (ambiguous); 2-keto-4-hydroxybutyrate aldolase (ambiguous); 4-hydroxy-2-oxoglutarate glyoxylate-lyase (ambiguous); eda (gene name)
Systematic name: (4S)-4-hydroxy-2-oxoglutarate glyoxylate-lyase (pyruvate-forming)
Comments: The enzyme from the bacterium Escherichia coli, which is specific for the (S)-enantiomer, is trifunctional, and also catalyses the reaction of EC 4.1.2.14, 2-dehydro-3-deoxy-phosphogluconate aldolase, and the β-decarboxylation of oxaloacetate. cf. EC 4.1.3.16, 4-hydroxy-2-oxoglutarate aldolase.
References:
1.  Nishihara, H. and Dekker, E.E. Purification, substrate specificity and binding, β-decarboxylase activity, and other properties of Escherichia coli 2-keto-4-hydroxyglutarate aldolase. J. Biol. Chem. 247 (1972) 5079–5087. [PMID: 4560498]
2.  Patil, R.V. and Dekker, E.E. Cloning, nucleotide sequence, overexpression, and inactivation of the Escherichia coli 2-keto-4-hydroxyglutarate aldolase gene. J. Bacteriol. 174 (1992) 102–107. [PMID: 1339418]
[EC 4.1.3.42 created 2013]
 
 
EC 4.1.3.43     
Accepted name: 4-hydroxy-2-oxohexanoate aldolase
Reaction: (S)-4-hydroxy-2-oxohexanoate = propanal + pyruvate
Other name(s): BphI
Systematic name: (S)-4-hydroxy-2-oxohexanoate pyruvate-lyase (propanal-forming)
Comments: Requires Mn2+ for maximal activity [1,2]. The enzymes from the bacteria Burkholderia xenovorans and Thermus thermophilus also perform the reaction of EC 4.1.3.39, 4-hydroxy-2-oxovalerate aldolase [1,2,6]. The enzyme forms a bifunctional complex with EC 1.2.1.87, propanal dehydrogenase (CoA-propanoylating), with a tight channel connecting the two subunits [3,4,6].
References:
1.  Baker, P., Pan, D., Carere, J., Rossi, A., Wang, W. and Seah, S.Y.K. Characterization of an aldolase-dehydrogenase complex that exhibits substrate channeling in the polychlorinated biphenyls degradation pathway. Biochemistry 48 (2009) 6551–6558. [PMID: 19476337]
2.  Wang, W., Baker, P. and Seah, S.Y.K. Comparison of two metal-dependent pyruvate aldolases related by convergent evolution: substrate specificity, kinetic mechanism, and substrate channeling. Biochemistry 49 (2010) 3774–3782. [PMID: 20364820]
3.  Baker, P., Carere, J. and Seah, S.Y.K. Probing the molecular basis of substrate specificity, stereospecificity, and catalysis in the class II pyruvate aldolase, BphI. Biochemistry 50 (2011) 3559–3569. [PMID: 21425833]
4.  Carere, J., Baker, P. and Seah, S.Y.K. Investigating the molecular determinants for substrate channeling in BphI-BphJ, an aldolase-dehydrogenase complex from the polychlorinated biphenyls degradation pathway. Biochemistry 50 (2011) 8407–8416. [PMID: 21838275]
5.  Baker, P. and Seah, S.Y.K. Rational design of stereoselectivity in the class II pyruvate aldolase BphI. J. Am. Chem. Soc. 134 (2012) 507–513. [PMID: 22081904]
6.  Baker, P., Hillis, C., Carere, J. and Seah, S.Y.K. Protein-protein interactions and substrate channeling in orthologous and chimeric aldolase-dehydrogenase complexes. Biochemistry 51 (2012) 1942–1952. [PMID: 22316175]
[EC 4.1.3.43 created 2013]
 
 
EC 4.1.3.44     
Accepted name: tRNA 4-demethylwyosine synthase (AdoMet-dependent)
Reaction: N1-methylguanine37 in tRNAPhe + pyruvate + S-adenosyl-L-methionine = 4-demethylwyosine37 in tRNAPhe + L-methionine + 5′-deoxyadenosine + CO2 + H2O
Glossary: 4-demethylwyosine = imG-14 = 6-methyl-3-(β-D-ribofuranosyl)-3,5-dihydro-9H-imidazo[1,2-a]purin-9-one
Other name(s): TYW1
Systematic name: tRNAPhe N1-methylguanine,pyruvate acetaldehyde-lyase (tRNAPhe 4-demethylwyosine-forming, decarboxylating, dehydrating)
Comments: This enzyme, which is a member of the superfamily of S-adenosyl-L-methionine-dependent radical (radical AdoMet) enzymes, binds two [4Fe-4S] clusters [3,4]. Carbons C2 and C3 from pyruvate are incorporated into 4-demethylwyosine [3]. The enzyme is found in eukaryotes where it is part of the pathway for wybutosine synthesis, and in archaea, where it is involved in the biosynthesis of archaeal wye bases, such as wyosine, isowyosine, and methylwyosine.
References:
1.  Goto-Ito, S., Ishii, R., Ito, T., Shibata, R., Fusatomi, E., Sekine, S.I., Bessho, Y. and Yokoyama, S. Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis. Acta Crystallogr. D Biol. Crystallogr. 63 (2007) 1059–1068. [PMID: 17881823]
2.  Suzuki, Y., Noma, A., Suzuki, T., Senda, M., Senda, T., Ishitani, R. and Nureki, O. Crystal structure of the radical SAM enzyme catalyzing tricyclic modified base formation in tRNA. J. Mol. Biol. 372 (2007) 1204–1214. [PMID: 17727881]
3.  Young, A.P. and Bandarian, V. Pyruvate is the source of the two carbons that are required for formation of the imidazoline ring of 4-demethylwyosine. Biochemistry 50 (2011) 10573–10575. [PMID: 22026549]
4.  Perche-Letuvée, P., Kathirvelu, V., Berggren, G., Clemancey, M., Latour, J.M., Maurel, V., Douki, T., Armengaud, J., Mulliez, E., Fontecave, M., Garcia-Serres, R., Gambarelli, S. and Atta, M. 4-Demethylwyosine synthase from Pyrococcus abyssi is a radical-S-adenosyl-L-methionine enzyme with an additional [4Fe-4S]2+ cluster that interacts with the pyruvate co-substrate. J. Biol. Chem. 287 (2012) 41174–41185. [PMID: 23043105]
[EC 4.1.3.44 created 2013]
 
 
EC 4.1.3.45     
Accepted name: 3-hydroxybenzoate synthase
Reaction: chorismate = 3-hydroxybenzoate + pyruvate
Glossary: chorismate = (3R,4R)-3-[(1-carboxyethenyl)oxy]-4-hydroxycyclohexa-1,5-diene-1-carboxylate
Other name(s): chorismatase/3-hydroxybenzoate synthase; hyg5 (gene name); bra8 (gene name); XanB2
Systematic name: chorismate pyruvate-lyase (3-hydroxybenzoate-forming)
Comments: The enzyme, found in several bacterial species is involved in biosynthesis of secondary products. The enzyme from the bacterium Xanthomonas campestris pv. campestris also has the activity of EC 4.1.3.40, chorismate lyase [3].
References:
1.  Andexer, J.N., Kendrew, S.G., Nur-e-Alam, M., Lazos, O., Foster, T.A., Zimmermann, A.S., Warneck, T.D., Suthar, D., Coates, N.J., Koehn, F.E., Skotnicki, J.S., Carter, G.T., Gregory, M.A., Martin, C.J., Moss, S.J., Leadlay, P.F. and Wilkinson, B. Biosynthesis of the immunosuppressants FK506, FK520, and rapamycin involves a previously undescribed family of enzymes acting on chorismate. Proc. Natl. Acad. Sci. USA 108 (2011) 4776–4781. [PMID: 21383123]
2.  Jiang, Y., Wang, H., Lu, C., Ding, Y., Li, Y. and Shen, Y. Identification and characterization of the cuevaene A biosynthetic gene cluster in Streptomyces sp. LZ35. ChemBioChem 14 (2013) 1468–1475. [PMID: 23824670]
3.  Zhou, L., Wang, J.Y., Wang, J., Poplawsky, A., Lin, S., Zhu, B., Chang, C., Zhou, T., Zhang, L.H. and He, Y.W. The diffusible factor synthase XanB2 is a bifunctional chorismatase that links the shikimate pathway to ubiquinone and xanthomonadins biosynthetic pathways. Mol. Microbiol. 87 (2013) 80–93. [PMID: 23113660]
[EC 4.1.3.45 created 2013]
 
 
EC 4.1.3.46     
Accepted name: (R)-citramalyl-CoA lyase
Reaction: (3R)-citramalyl-CoA = acetyl-CoA + pyruvate
Other name(s): Ccl
Systematic name: (3R)-citramalyl-CoA pyruvate-lyase (acetyl-CoA-forming)
Comments: Requires Mn2+ ions for activity. The enzyme, purified from the bacterium Chloroflexus aurantiacus, has no activity with (3S)-citramalyl-CoA (cf. EC 4.1.3.25, (S)-citramalyl-CoA lyase).
References:
1.  Friedmann, S., Alber, B.E. and Fuchs, G. Properties of R-citramalyl-coenzyme A lyase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus. J. Bacteriol. 189 (2007) 2906–2914. [PMID: 17259315]
[EC 4.1.3.46 created 2014]
 
 
EC 4.1.99.1     
Accepted name: tryptophanase
Reaction: L-tryptophan + H2O = indole + pyruvate + NH3 (overall reaction)
(1a) L-tryptophan = indole + 2-aminoprop-2-enoate
(1b) 2-aminoprop-2-enoate = 2-iminopropanoate (spontaneous)
(1c) 2-iminopropanoate + H2O = pyruvate + NH3 (spontaneous)
Other name(s): L-tryptophanase; L-tryptophan indole-lyase (deaminating); TNase
Systematic name: L-tryptophan indole-lyase (deaminating; pyruvate-forming)
Comments: A pyridoxal-phosphate protein, requiring K+. The enzyme cleaves a carbon-carbon bond, releasing indole and an unstable enamine product that tautomerizes to an imine form, which undergoes a hydrolytic deamination to form pyruvate and ammonia. The latter reaction, which can occur spontaneously, can also be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate deaminase. Also catalyses 2,3-elimination and β-replacement reactions of some indole-substituted tryptophan analogues of L-cysteine, L-serine and other 3-substituted amino acids.
References:
1.  Burns, R.O. and DeMoss, R.D. Properties of tryptophanase from Escherichia coli. Biochim. Biophys. Acta 65 (1962) 233–244. [PMID: 14017164]
2.  Newton, W.A., Morino, Y. and Snell, E.E. Properties of crystalline tryptophanase. J. Biol. Chem. 240 (1965) 1211–1218. [PMID: 14284727]
3.  Cowell, J.L., Maser, K. and DeMoss, R.D. Tryptophanase from Aeromonas liquifaciens. Purification, molecular weight and some chemical, catalytic and immunological properties. Biochim. Biophys. Acta 315 (1973) 449–463.
4.  Snell, E.E. Tryptophanase: structure, catalytic activities, and mechanism of action. Adv. Enzymol. Relat. Areas Mol. Biol. 42 (1975) 287–333. [PMID: 236639]
[EC 4.1.99.1 created 1972]
 
 
EC 4.1.99.2     
Accepted name: tyrosine phenol-lyase
Reaction: L-tyrosine + H2O = phenol + pyruvate + NH3 (overall reaction)
(1a) L-tyrosine = phenol + 2-aminoprop-2-enoate
(1b) 2-aminoprop-2-enoate = 2-iminopropanoate (spontaneous)
(1c) 2-iminopropanoate + H2O = pyruvate + NH3 (spontaneous)
Other name(s): β-tyrosinase; L-tyrosine phenol-lyase (deaminating)
Systematic name: L-tyrosine phenol-lyase (deaminating; pyruvate-forming)
Comments: A pyridoxal-phosphate protein. The enzyme cleaves a carbon-carbon bond, releasing phenol and an unstable enamine product that tautomerizes to an imine form, which undergoes a hydrolytic deamination to form pyruvate and ammonia. The latter reaction, which can occur spontaneously, can also be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate deaminase. The enzyme also slowly catalyses similar reactions with D-tyrosine, S-methyl-L-cysteine, L-cysteine, L-serine and D-serine.
References:
1.  Kumagai, H., Yamada, H., Matsui, H., Ohkishi, H. and Ogata, K. Tyrosine phenol lyase. I. Purification, crystallization, and properties. J. Biol. Chem. 245 (1970) 1767–1772. [PMID: 4908868]
2.  Kumagai, H., Yamada, H., Matsui, H., Ohkishi, H. and Ogata, K. Tyrosine phenol lyase. II. Cofactor requirements. J. Biol. Chem. 245 (1970) 1773–1777. [PMID: 4908869]
[EC 4.1.99.2 created 1972]
 
 
EC 4.1.99.3     
Accepted name: deoxyribodipyrimidine photo-lyase
Reaction: cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA)
Other name(s): photoreactivating enzyme; DNA photolyase; DNA-photoreactivating enzyme; DNA cyclobutane dipyrimidine photolyase; DNA photolyase; deoxyribonucleic photolyase; deoxyribodipyrimidine photolyase; photolyase; PRE; PhrB photolyase; deoxyribonucleic cyclobutane dipyrimidine photolyase; phr A photolyase; dipyrimidine photolyase (photosensitive); deoxyribonucleate pyrimidine dimer lyase (photosensitive)
Systematic name: deoxyribocyclobutadipyrimidine pyrimidine-lyase
Comments: A flavoprotein (FAD), containing a second chromophore group. The enzyme catalyses the reactivation by light of irradiated DNA. A similar reactivation of irradiated RNA is probably due to a separate enzyme.
References:
1.  Eker, A.P.M. and Fichtinger-Schepman, A.M.J. Studies on a DNA photoreactivating enzyme from Streptomyces griseus. II. Purification of the enzyme. Biochim. Biophys. Acta 378 (1975) 54–63. [PMID: 804322]
2.  Sancar, G.B., Smith, F.W., Reid, R., Payne, G., Levy, M. and Sancar, A. Action mechanism of Escherichia coli DNA photolyase. I. Formation of the enzyme-substrate complex. J. Biol. Chem. 262 (1987) 478–485. [PMID: 3539939]
3.  Setlow, J.K. and Bollum, F.J. The minimum size of the substrate for yeast photoreactivating enzyme. Biochim. Biophys. Acta 157 (1968) 233–237. [PMID: 5649902]
[EC 4.1.99.3 created 1972]
 
 
EC 4.1.99.4      
Transferred entry: 1-aminocyclopropane-1-carboxylate deaminase. Now EC 3.5.99.7, 1-aminocyclopropane-1-carboxylate deaminase
[EC 4.1.99.4 created 1981, deleted 2002]
 
 
EC 4.1.99.5     
Accepted name: aldehyde oxygenase (deformylating)
Reaction: a long-chain aldehyde + O2 + 2 NADPH + 2 H+ = an alkane + formate + H2O + 2 NADP+
Glossary: a long-chain aldehyde = an aldehyde derived from a fatty acid with an aliphatic chain of 13-22 carbons.
Other name(s): decarbonylase; aldehyde decarbonylase; octadecanal decarbonylase; octadecanal alkane-lyase
Systematic name: a long-chain aldehyde alkane-lyase
Comments: Contains a diiron center. Involved in the biosynthesis of alkanes. The enzyme from the cyanobacterium Nostoc punctiforme PCC 73102 is only active in vitro in the presence of ferredoxin, ferredoxin reductase and NADPH, and produces mostly C15 and C17 alkanes [2,3]. The enzyme from pea (Pisum sativum) produces alkanes of chain length C18 to C32 and is inhibited by metal-chelating agents [1]. The substrate for this enzyme is formed by EC 1.2.1.80, acyl-[acyl-carrier protein] reductase.
References:
1.  Cheesbrough, T.M. and, K olattukudy, P.E. Alkane biosynthesis by decarbonylation of aldehydes catalyzed by a particulate preparation from Pisum sativum. Proc. Natl. Acad. Sci. USA 81 (1984) 6613–6617. [PMID: 6593720]
2.  Schirmer, A., Rude, M.A., Li, X., Popova, E. and del Cardayre, S.B. Microbial biosynthesis of alkanes. Science 329 (2010) 559–562. [PMID: 20671186]
3.  Warui, D.M., Li, N., Nørgaard, H., Krebs, C., Bollinger, J.M. and Booker, S.J. Detection of formate, rather than carbon monoxide, as the stoichiometric coproduct in conversion of fatty aldehydes to alkanes by a cyanobacterial aldehyde decarbonylase. J. Am. Chem. Soc. 133 (2011) 3316–3319. [PMID: 21341652]
4.  Li, N., Chang, W.C., Warui, D.M., Booker, S.J., Krebs, C. and Bollinger, J.M., Jr. Evidence for only oxygenative cleavage of aldehydes to alk(a/e)nes and formate by cyanobacterial aldehyde decarbonylases. Biochemistry 51 (2012) 7908–7916. [PMID: 22947199]
[EC 4.1.99.5 created 1989, modified 2011, modified 2013]
 
 
EC 4.1.99.6      
Transferred entry: trichodiene synthase. Now EC 4.2.3.6, trichodiene synthase
[EC 4.1.99.6 created 1989, deleted 2000]
 
 
EC 4.1.99.7      
Transferred entry: aristolochene synthase. Now EC 4.2.3.9, aristolochene synthase
[EC 4.1.99.7 created 1992 as EC 2.5.1.40, transferred 1999 to EC 4.1.99.7, deleted 2000]
 
 
EC 4.1.99.8      
Transferred entry: pinene synthase. Now EC 4.2.3.14, pinene synthase
[EC 4.1.99.8 created 2000, deleted 2000]
 
 
EC 4.1.99.9      
Transferred entry: myrcene synthase. Now EC 4.2.3.15, myrcene synthase
[EC 4.1.99.9 created 2000, deleted 2000]
 
 
EC 4.1.99.10      
Transferred entry: (-)-(4S)-limonene synthase. Now EC 4.2.3.16, (4S)-limonene synthase
[EC 4.1.99.10 created 2000, deleted 2000]
 
 
EC 4.1.99.11     
Accepted name: benzylsuccinate synthase
Reaction: benzylsuccinate = toluene + fumarate
Other name(s): benzylsuccinate fumarate-lyase
Systematic name: benzylsuccinate fumarate-lyase (toluene-forming)
Comments: A glycyl radical enzyme that is inhibited by benzyl alcohol, benzaldehyde, phenylhydrazine and is inactivated by oxygen.
References:
1.  Beller, H.R. and Spormann, A.M. Analysis of the novel benzylsuccinate synthase reaction for anaerobic toluene activation based on structural studies of the product. J. Bacteriol. 180 (1998) 5454–5457. [PMID: 9765580]
2.  Leuthner, B., Leutwein, C., Schultz, H., Hörth, P., Haehnel, W., Schiltz, E., Schägger, H. and Heider, J. Biochemical and genetic characterisation of benzylsuccinate synthase from Thauera aromatica: a new glycyl radical enzyme catalysing the first step in anaerobic toluene metabolism. Mol. Microbiol. 28 (1998) 615–628. [PMID: 9632263]
[EC 4.1.99.11 created 2000]
 
 
EC 4.1.99.12     
Accepted name: 3,4-dihydroxy-2-butanone-4-phosphate synthase
Reaction: D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate
Other name(s): DHBP synthase; L-3,4-dihydroxybutan-2-one-4-phosphate synthase
Systematic name: D-ribulose 5-phosphate formate-lyase (L-3,4-dihydroxybutan-2-one 4-phosphate-forming)
Comments: Requires a divalent cation, preferably Mg2+, for activity [1]. The reaction involves an intramolecular skeletal rearrangement, with the bonds in D-ribulose 5-phosphate that connect C-3 and C-5 to C-4 being broken, C-4 being removed as formate and reconnection of C-3 and C-5 [1]. The phosphorylated four-carbon product (L-3,4-dihydroxybutan-2-one 4-phosphate) is an intermediate in the biosynthesis of riboflavin [1].
References:
1.  Volk, R. and Bacher, A. Studies on the 4-carbon precursor in the biosynthesis of riboflavin. Purification and properties of L-3,4-dihydroxy-2-butanone-4-phosphate synthase. J. Biol. Chem. 265 (1990) 19479–19485. [PMID: 2246238]
2.  Liao, D.I., Calabrese, J.C., Wawrzak, Z., Viitanen, P.V. and Jordan, D.B. Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase of riboflavin biosynthesis. Structure 9 (2001) 11–18. [PMID: 11342130]
3.  Kelly, M.J., Ball, L.J., Krieger, C., Yu, Y., Fischer, M., Schiffmann, S., Schmieder, P., Kühne, R., Bermel, W., Bacher, A., Richter, G. and Oschkinat, H. The NMR structure of the 47-kDa dimeric enzyme 3,4-dihydroxy-2-butanone-4-phosphate synthase and ligand binding studies reveal the location of the active site. Proc. Natl. Acad. Sci. USA 98 (2001) 13025–13030. [PMID: 11687623]
4.  Liao, D.I., Zheng, Y.J., Viitanen, P.V. and Jordan, D.B. Structural definition of the active site and catalytic mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase. Biochemistry 41 (2002) 1795–1806. [PMID: 11827524]
5.  Fischer, M., Römisch, W., Schiffmann, S., Kelly, M., Oschkinat, H., Steinbacher, S., Huber, R., Eisenreich, W., Richter, G. and Bacher, A. Biosynthesis of riboflavin in archaea studies on the mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase of Methanococcus jannaschii. J. Biol. Chem. 277 (2002) 41410–41416. [PMID: 12200440]
6.  Steinbacher, S., Schiffmann, S., Richter, G., Huber, R., Bacher, A. and Fischer, M. Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and the substrate ribulose 5-phosphate: implications for the catalytic mechanism. J. Biol. Chem. 278 (2003) 42256–42265. [PMID: 12904291]
7.  Steinbacher, S., Schiffmann, S., Bacher, A. and Fischer, M. Metal sites in 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with the substrate ribulose 5-phosphate. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 1338–1340. [PMID: 15213409]
8.  Echt, S., Bauer, S., Steinbacher, S., Huber, R., Bacher, A. and Fischer, M. Potential anti-infective targets in pathogenic yeasts: structure and properties of 3,4-dihydroxy-2-butanone 4-phosphate synthase of Candida albicans. J. Mol. Biol. 341 (2004) 1085–1096. [PMID: 15328619]
[EC 4.1.99.12 created 2007]
 
 
EC 4.1.99.13     
Accepted name: (6-4)DNA photolyase
Reaction: (6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
Other name(s): DNA photolyase; H64PRH; NF-10; phr (6-4); PL-(6-4); OtCPF1; (6-4) PHR; At64PHR
Systematic name: (6-4) photoproduct pyrimidine-lyase
Comments: A flavoprotein (FAD). The overall repair reaction consists of two distinct steps, one of which is light-independent and the other one light-dependent. In the initial light-independent step, a 6-iminium ion is thought to be generated via proton transfer induced by two histidines highly conserved among the (6-4) photolyases. This intermediate spontaneously rearranges to form an oxetane intermediate by intramolecular nucleophilic attack. In the subsequent light-driven reaction, one electron is believed to be transferred from the fully reduced FAD cofactor (FADH-) to the oxetane intermediate thus forming a neutral FADH radical and an anionic oxetane radical, which spontaneously fractures. The excess electron is then back-transferred to the flavin radical restoring the fully reduced flavin cofactor and a pair of pyrimidine bases [2].
References:
1.  Hitomi, K., DiTacchio, L., Arvai, A.S., Yamamoto, J., Kim, S.T., Todo, T., Tainer, J.A., Iwai, S., Panda, S. and Getzoff, E.D. Functional motifs in the (6-4) photolyase crystal structure make a comparative framework for DNA repair photolyases and clock cryptochromes. Proc. Natl. Acad. Sci. USA 106 (2009) 6962–6967. [PMID: 19359474]
2.  Schleicher, E., Hitomi, K., Kay, C.W., Getzoff, E.D., Todo, T. and Weber, S. Electron nuclear double resonance differentiates complementary roles for active site histidines in (6-4) photolyase. J. Biol. Chem. 282 (2007) 4738–4747. [PMID: 17164245]
[EC 4.1.99.13 created 2009]
 
 
EC 4.1.99.14     
Accepted name: spore photoproduct lyase
Reaction: (5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3′→5′)-thymidylate (in double-helical DNA)
Other name(s): SAM; SP lyase; SPL; SplB; SplG
Systematic name: spore photoproduct pyrimidine-lyase
Comments: This enzyme is a member of the ’AdoMet radical’ (radical SAM) family. The enzyme binds a [4Fe-4S] cluster. The cluster is coordinated by 3 cysteines and an exchangeable SAM molecule [3]. The 5′-deoxy-adenosine radical formed after electron transfer from the [4Fe-4S] cluster to the S-adenosyl-L-methionine, initiates the repair by abstracting the C-6 hydrogen of the spore photoproduct lesion. During the second part of the repair process the SAM molecule is regenerated [3].
References:
1.  Chandor, A., Berteau, O., Douki, T., Gasparutto, D., Sanakis, Y., Ollagnier-de-Choudens, S., Atta, M. and Fontecave, M. Dinucleotide spore photoproduct, a minimal substrate of the DNA repair spore photoproduct lyase enzyme from Bacillus subtilis. J. Biol. Chem. 281 (2006) 26922–26931. [PMID: 16829676]
2.  Pieck, J.C., Hennecke, U., Pierik, A.J., Friedel, M.G. and Carell, T. Characterization of a new thermophilic spore photoproduct lyase from Geobacillus stearothermophilus (SplG) with defined lesion containing DNA substrates. J. Biol. Chem. 281 (2006) 36317–36326. [PMID: 16968710]
3.  Buis, J.M., Cheek, J., Kalliri, E. and Broderick, J.B. Characterization of an active spore photoproduct lyase, a DNA repair enzyme in the radical S-adenosylmethionine superfamily. J. Biol. Chem. 281 (2006) 25994–26003. [PMID: 16829680]
4.  Mantel, C., Chandor, A., Gasparutto, D., Douki, T., Atta, M., Fontecave, M., Bayle, P.-A., Mouesca, J.-M. and Bardet, M. Combined NMR and DFT studies for the absolute configuration elucidation of the spore photoproduct, a UV-induced DNA lesion. J. Am. Chem. Soc. 130 (2008) 16978–16984. [PMID: 19012397]
5.  Silver, S.C., Chandra, T., Zilinskas, E., Ghose, S., Broderick, W.E. and Broderick, J.B. Complete stereospecific repair of a synthetic dinucleotide spore photoproduct by spore photoproduct lyase. J. Biol. Inorg. Chem. 15 (2010) 943–955. [PMID: 20405152]
[EC 4.1.99.14 created 2009, modified 2010]
 
 
EC 4.1.99.15      
Deleted entry: S-specific spore photoproduct lyase. This enzyme was classified on the basis of an incorrect reaction. The activity is covered by EC 4.1.99.14, spore photoproduct lyase
[EC 4.1.99.15 created 2009, deleted 2010]
 
 
EC 4.1.99.16     
Accepted name: geosmin synthase
Reaction: (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + H2O = (-)-geosmin + acetone
Systematic name: germacradienol geosmin-lyase (acetone forming)
Comments: Requires Mg2+. Geosmin is the cause of the characteristic smell of moist soil. It is a bifunctional enzyme. The N-terminal part of the enzyme is EC 4.2.3.22, germacradienol synthase, and forms germacradienol from FPP. The C-terminal part of the enzyme catalyses the conversion of germacradienol to geosmin via (1S,4aS,8aS)-1,4a-dimethyl-1,2,3,4,4a,5,6,8a-octahydronaphthalene.
References:
1.  Jiang, J., He, X. and Cane, D.E. Geosmin biosynthesis. Streptomyces coelicolor germacradienol/germacrene D synthase converts farnesyl diphosphate to geosmin. J. Am. Chem. Soc. 128 (2006) 8128–8129. [PMID: 16787064]
2.  Cane, D.E., He, X., Kobayashi, S., Omura, S. and Ikeda, H. Geosmin biosynthesis in Streptomyces avermitilis. Molecular cloning, expression, and mechanistic study of the germacradienol/geosmin synthase. J. Antibiot. (Tokyo) 59 (2006) 471–479. [PMID: 17080683]
3.  Jiang, J., He, X. and Cane, D.E. Biosynthesis of the earthy odorant geosmin by a bifunctional Streptomyces coelicolor enzyme. Nat. Chem. Biol. 3 (2007) 711–715. [PMID: 17873868]
[EC 4.1.99.16 created 2011]
 
 
EC 4.1.99.17     
Accepted name: phosphomethylpyrimidine synthase
Reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 5′-deoxyadenosine + L-methionine + formate + CO
Other name(s): thiC (gene name)
Systematic name: 5-amino-1-(5-phospho-D-ribosyl)imidazole formate-lyase (decarboxylating, 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine-forming)
Comments: Binds a [4Fe-4S] cluster that is coordinated by 3 cysteines and an exchangeable S-adenosyl-L-methionine molecule. The first stage of catalysis is reduction of the S-adenosyl-L-methionine to produce L-methionine and a 5′-deoxyadenosin-5′-yl radical that is crucial for the conversion of the substrate. Part of the pathway for thiamine biosynthesis.
References:
1.  Chatterjee, A., Li, Y., Zhang, Y., Grove, T.L., Lee, M., Krebs, C., Booker, S.J., Begley, T.P. and Ealick, S.E. Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily. Nat. Chem. Biol. 4 (2008) 758–765. [PMID: 18953358]
2.  Martinez-Gomez, N.C., Poyner, R.R., Mansoorabadi, S.O., Reed, G.H. and Downs, D.M. Reaction of AdoMet with ThiC generates a backbone free radical. Biochemistry 48 (2009) 217–219. [PMID: 19113839]
3.  Chatterjee, A., Hazra, A.B., Abdelwahed, S., Hilmey, D.G. and Begley, T.P. A "radical dance" in thiamin biosynthesis: mechanistic analysis of the bacterial hydroxymethylpyrimidine phosphate synthase. Angew. Chem. Int. Ed. Engl. 49 (2010) 8653–8656. [PMID: 20886485]
[EC 4.1.99.17 created 2011]
 
 
EC 4.1.99.18      
Transferred entry: cyclic pyranopterin phosphate synthase. Now known to be catalysed by the combined effort of EC 4.1.99.22, GTP 3,8-cyclase, and EC 4.6.1.17, cyclic pyranopterin monophosphate synthase
[EC 4.1.99.18 created 2011, deleted 2016]
 
 
EC 4.1.99.19     
Accepted name: 2-iminoacetate synthase
Reaction: L-tyrosine + S-adenosyl-L-methionine + NADPH = 2-iminoacetate + 4-methylphenol + 5′-deoxyadenosine + L-methionine + NADP+ + H+
Glossary: 4-methylphenol = 4-cresol = p-cresol
Other name(s): thiH (gene name)
Systematic name: L-tyrosine 4-methylphenol-lyase (2-iminoacetate-forming)
Comments: Binds a [4Fe-4S] cluster that is coordinated by 3 cysteines and an exchangeable S-adenosyl-L-methionine molecule. The first stage of catalysis is reduction of the S-adenosyl-L-methionine to produce methionine and a 5-deoxyadenosin-5-yl radical that is crucial for the conversion of the substrate. The reductant is assumed to be NADPH, which is provided by a flavoprotein:NADPH oxidoreductase system [4]. Part of the pathway for thiamine biosynthesis.
References:
1.  Leonardi, R., Fairhurst, S.A., Kriek, M., Lowe, D.J. and Roach, P.L. Thiamine biosynthesis in Escherichia coli: isolation and initial characterisation of the ThiGH complex. FEBS Lett. 539 (2003) 95–99. [PMID: 12650933]
2.  Kriek, M., Martins, F., Challand, M.R., Croft, A. and Roach, P.L. Thiamine biosynthesis in Escherichia coli: identification of the intermediate and by-product derived from tyrosine. Angew. Chem. Int. Ed. Engl. 46 (2007) 9223–9226. [PMID: 17969213]
3.  Kriek, M., Martins, F., Leonardi, R., Fairhurst, S.A., Lowe, D.J. and Roach, P.L. Thiazole synthase from Escherichia coli: an investigation of the substrates and purified proteins required for activity in vitro. J. Biol. Chem. 282 (2007) 17413–17423. [PMID: 17403671]
4.  Challand, M.R., Martins, F.T. and Roach, P.L. Catalytic activity of the anaerobic tyrosine lyase required for thiamine biosynthesis in Escherichia coli. J. Biol. Chem. 285 (2010) 5240–5248. [PMID: 19923213]
[EC 4.1.99.19 created 2011, modified 2014]
 
 
EC 4.1.99.20     
Accepted name: 3-amino-4-hydroxybenzoate synthase
Reaction: 2-amino-4,5-dihydroxy-6-oxo-7-(phosphooxy)heptanoate = 3-amino-4-hydroxybenzoate + phosphate + 2 H2O
Other name(s): 3,4-AHBA synthase; griH (gene name)
Systematic name: 2-amino-4,5-dihydroxy-6-oxo-7-(phosphooxy)heptanoate hydro-lyase (cyclizing, 3-amino-4-hydroxybenzoate-forming)
Comments: Requires Mn2+ for maximum activity. The reaction is suggested to take place in several steps. Schiff base formation, double bond migration and dephosphorylation followed by ring opening and closing to form a pyrrolidine ring, and finally dehydration to form the product 3-amino-4-hydroxybenzoate. In the bacterium Streptomyces griseus the enzyme is involved in biosynthesis of grixazone, a yellow pigment that contains a phenoxazinone chromophore.
References:
1.  Suzuki, H., Ohnishi, Y., Furusho, Y., Sakuda, S. and Horinouchi, S. Novel benzene ring biosynthesis from C3 and C4 primary metabolites by two enzymes. J. Biol. Chem. 281 (2006) 36944–36951. [PMID: 17003031]
[EC 4.1.99.20 created 2013, modified 2016]
 
 
EC 4.1.99.21      
Transferred entry: (5-formylfuran-3-yl)methyl phosphate synthase. Now EC 4.2.3.153 (5-formylfuran-3-yl)methyl phosphate synthase.
[EC 4.1.99.21 created 2015, deleted 2015]
 
 
EC 4.1.99.22     
Accepted name: GTP 3′,8-cyclase
Reaction: GTP + S-adenosyl-L-methionine + reduced electron acceptor = (8S)-3′,8-cyclo-7,8-dihydroguanosine 5′-triphosphate + 5′-deoxyadenosine + L-methionine + oxidized electron acceptor
Other name(s): MOCS1A (gene name); moaA (gene name); cnx2 (gene name)
Systematic name: GTP 3′,8-cyclase [(8S)-3′,8-cyclo-7,8-dihydroguanosine 5′-triphosphate-forming]
Comments: The enzyme catalyses an early step in the biosynthesis of the molybdenum cofactor (MoCo). In bacteria and plants the reaction is catalysed by MoaA and Cnx2, respectively. In mammals it is catalysed by the MOCS1A domain of the bifunctional MOCS1 protein, which also catalyses EC 4.6.1.17, cyclic pyranopterin monophosphate synthase. The enzyme belongs to the superfamily of radical S-adenosyl-L-methionine (radical SAM) enzymes, and contains two oxygen-sensitive FeS clusters.
References:
1.  Hänzelmann, P., Hernandez, H.L., Menzel, C., Garcia-Serres, R., Huynh, B.H., Johnson, M.K., Mendel, R.R. and Schindelin, H. Characterization of MOCS1A, an oxygen-sensitive iron-sulfur protein involved in human molybdenum cofactor biosynthesis. J. Biol. Chem. 279 (2004) 34721–34732. [PMID: 15180982]
2.  Hänzelmann, P. and Schindelin, H. Crystal structure of the S-adenosylmethionine-dependent enzyme MoaA and its implications for molybdenum cofactor deficiency in humans. Proc. Natl. Acad. Sci. USA 101 (2004) 12870–12875. [PMID: 15317939]
3.  Hänzelmann, P. and Schindelin, H. Binding of 5′-GTP to the C-terminal FeS cluster of the radical S-adenosylmethionine enzyme MoaA provides insights into its mechanism. Proc. Natl. Acad. Sci. USA 103 (2006) 6829–6834. [PMID: 16632608]
4.  Lees, N.S., Hänzelmann, P., Hernandez, H.L., Subramanian, S., Schindelin, H., Johnson, M.K. and Hoffman, B.M. ENDOR spectroscopy shows that guanine N1 binds to [4Fe-4S] cluster II of the S-adenosylmethionine-dependent enzyme MoaA: mechanistic implications. J. Am. Chem. Soc. 131 (2009) 9184–9185. [PMID: 19566093]
5.  Hover, B.M., Loksztejn, A., Ribeiro, A.A. and Yokoyama, K. Identification of a cyclic nucleotide as a cryptic intermediate in molybdenum cofactor biosynthesis. J. Am. Chem. Soc. 135 (2013) 7019–7032. [PMID: 23627491]
6.  Hover, B.M. and Yokoyama, K. C-Terminal glycine-gated radical initiation by GTP 3′,8-cyclase in the molybdenum cofactor biosynthesis. J. Am. Chem. Soc. 137 (2015) 3352–3359. [PMID: 25697423]
7.  Hover, B.M., Tonthat, N.K., Schumacher, M.A. and Yokoyama, K. Mechanism of pyranopterin ring formation in molybdenum cofactor biosynthesis. Proc. Natl. Acad. Sci. USA 112 (2015) 6347–6352. [PMID: 25941396]
[EC 4.1.99.22 created 2011 as EC 4.1.99.18, part transferred 2016 to EC 4.1.99.22]
 
 
EC 4.1.99.23     
Accepted name: 5-hydroxybenzimidazole synthase
Reaction: 5-amino-1-(5-phospho-β-D-ribosyl)imidazole + S-adenosyl-L-methionine + reduced acceptor = 5-hydroxybenzimidazole + 5′-deoxyadenosine + L-methionine + formate + NH3 + phosphate + oxidized acceptor
Other name(s): bzaF (gene name); HBI synthase
Systematic name: 5-amino-1-(5-phospho-β-D-ribosyl)imidazole formate-lyase (5-hydroxybenzimidazole-forming)
Comments: The enzyme, purified from bacteria, is part of the anaerobic pathway for cobalamin biosynthesis. It binds a [4Fe-4S] cluster that is coordinated by 3 cysteines and an exchangeable S-adenosyl-L-methionine molecule. The first stage of catalysis is reduction of the S-adenosyl-L-methionine to produce L-methionine and a 5′-deoxyadenosin-5′-yl radical that is crucial for the conversion of the substrate.
References:
1.  Mehta, A.P., Abdelwahed, S.H., Fenwick, M.K., Hazra, A.B., Taga, M.E., Zhang, Y., Ealick, S.E. and Begley, T.P. Anaerobic 5-hydroxybenzimidazole formation from aminoimidazole ribotide: an unanticipated intersection of thiamin and vitamin B12 biosynthesis. J. Am. Chem. Soc. 137 (2015) 10444–10447. [PMID: 26237670]
2.  Hazra, A.B., Han, A.W., Mehta, A.P., Mok, K.C., Osadchiy, V., Begley, T.P. and Taga, M.E. Anaerobic biosynthesis of the lower ligand of vitamin B12. Proc. Natl. Acad. Sci. USA 112 (2015) 10792–10797. [PMID: 26246619]
[EC 4.1.99.23 created 2017]
 
 
EC 4.1.99.24     
Accepted name: L-tyrosine isonitrile synthase
Reaction: L-tyrosine + D-ribulose 5-phosphate = (2S)-3-(4-hydroxyphenyl)-2-isocyanopropanoate + hydroxyacetone + formaldehyde + phosphate + H2O
Glossary: (2S)-3-(4-hydroxyphenyl)-2-isocyanopropanoate = L-tyrosine isonitrile
paerucumarin = 6,7-dihydroxy-3-isocyanochromen-2-one
rhabduscin = N-[(2S,3S,4R,5S,6R)-4,5-dihydroxy-6-{4-[(E)-2-isocyanoethenyl]phenoxy}-2-methyloxan-3-yl]acetamide
Other name(s): pvcA (gene name)
Systematic name: L-tyrosine:D-ribulose-5-phosphate lyase (isonitrile-forming)
Comments: The enzymes from the bacteria Pseudomonas aeruginosa and Xenorhabdus nematophila are involved in the biosynthesis of paerucumarin and rhabduscin, respectively. According to the proposed mechanism, the enzyme forms an imine intermediate composed of linked L-tyrosine and D-ribulose 5-phosphate, followed by loss of the phosphate group and formation of a β-keto imine and keto-enol tautomerization. This is followed by a C-C bond cleavage, the release of hydroxyacetone, and a retro aldol type reaction that releases formaldehyde and forms the final product [3]. cf. EC 4.1.99.25, L-tryptophan isonitrile synthase.
References:
1.  Clarke-Pearson, M.F. and Brady, S.F. Paerucumarin, a new metabolite produced by the pvc gene cluster from Pseudomonas aeruginosa. J. Bacteriol. 190 (2008) 6927–6930. [PMID: 18689486]
2.  Drake, E.J. and Gulick, A.M. Three-dimensional structures of Pseudomonas aeruginosa PvcA and PvcB, two proteins involved in the synthesis of 2-isocyano-6,7-dihydroxycoumarin. J. Mol. Biol. 384 (2008) 193–205. [PMID: 18824174]
3.  Chang, W.C., Sanyal, D., Huang, J.L., Ittiamornkul, K., Zhu, Q. and Liu, X. In vitro stepwise reconstitution of amino acid derived vinyl isocyanide biosynthesis: detection of an elusive intermediate. Org. Lett. 19 (2017) 1208–1211. [PMID: 28212039]
[EC 4.1.99.24 created 2018]
 
 
EC 4.1.99.25     
Accepted name: L-tryptophan isonitrile synthase
Reaction: L-tryptophan + D-ribulose 5-phosphate = (2S)-3-(1H-indol-3-yl)-2-isocyanopropanoate + hydroxyacetone + formaldehyde + phosphate + H2O
Glossary: (2S)-3-(1H-indol-3-yl)-2-isocyanopropanoate = L-tryptophan isonitrile
hydroxyacetone = 1-hydroxypropan-2-one
Other name(s): isnA (gene name); ambI1 (gene name); well1 (gene name)
Systematic name: L-tryptophan:D-ribulose-5-phosphate lyase (isonitrile-forming)
Comments: The enzymes from cyanobacteria that belong to the Nostocales order participate in the biosynthesis of hapalindole-type alkaloids. According to the proposed mechanism, the enzyme forms an imine intermediate composed of linked L-tryptophan and D-ribulose 5-phosphate, followed by loss of the phosphate group and formation of a β-keto imine and keto-enol tautomerization. This is followed by a C-C bond cleavage, the release of hydroxyacetone, and a retro aldol type reaction that releases formaldehyde and forms the final product [3]. cf. EC 4.1.99.24, L-tyrosine isonitrile synthase.
References:
1.  Brady, S.F. and Clardy, J. Cloning and heterologous expression of isocyanide biosynthetic genes from environmental DNA. Angew. Chem. Int. Ed. Engl. 44 (2005) 7063–7065. [PMID: 16206308]
2.  Brady, S.F. and Clardy, J. Systematic investigation of the Escherichia coli metabolome for the biosynthetic origin of an isocyanide carbon atom. Angew. Chem. Int. Ed. Engl. 44 (2005) 7045–7048. [PMID: 16217820]
3.  Hillwig, M.L., Zhu, Q. and Liu, X. Biosynthesis of ambiguine indole alkaloids in cyanobacterium Fischerella ambigua. ACS Chem. Biol. 9 (2014) 372–377. [PMID: 24180436]
4.  Chang, W.C., Sanyal, D., Huang, J.L., Ittiamornkul, K., Zhu, Q. and Liu, X. In vitro stepwise reconstitution of amino acid derived vinyl isocyanide biosynthesis: detection of an elusive intermediate. Org. Lett. 19 (2017) 1208–1211. [PMID: 28212039]
[EC 4.1.99.25 created 2018]
 
 
EC 4.2.1.1     
Accepted name: carbonic anhydrase
Reaction: H2CO3 = CO2 + H2O
Other name(s): carbonate dehydratase; anhydrase; carbonate anhydrase; carbonic acid anhydrase; carboxyanhydrase; carbonic anhydrase A; carbonate hydro-lyase; carbonate hydro-lyase (carbon-dioxide-forming)
Systematic name: carbonic acid hydro-lyase (carbon-dioxide-forming)
Comments: The enzyme catalyses the reversible hydration of gaseous CO2 to carbonic acid, which dissociates to give hydrogencarbonate above neutral pH. It is widespread and found in archaea, bacteria, and eukaryotes. Three distinct classes exist, and appear to have evolved independently. Contains zinc.
References:
1.  Keilin, D. and Mann, T. Carbonic anhydrase. Nature 144 (1939) 442–443.
2.  Kannan, K.K., Ramanadham, M. and Jones, T.A. Structure, refinement, and function of carbonic anhydrase isozymes: refinement of human carbonic anhydrase I. Ann. N.Y. Acad. Sci. 429 (1984) 49–60. [PMID: 6430186]
3.  Murakami, H. and Sly, W.S. Purification and characterization of human salivary carbonic anhydrase. J. Biol. Chem. 262 (1987) 1382–1388. [PMID: 2433278]
4.  Iverson, T.M., Alber, B.E., Kisker, C., Ferry, J.G. and Rees, D.C. A closer look at the active site of γ-class carbonic anhydrases: high-resolution crystallographic studies of the carbonic anhydrase from Methanosarcina thermophila. Biochemistry 39 (2000) 9222–9231. [PMID: 10924115]
5.  Smith, K.S. and Ferry, J.G. Prokaryotic carbonic anhydrases. FEMS Microbiol. Rev. 24 (2000) 335–366. [PMID: 10978542]
6.  Cronk, J.D., Endrizzi, J.A., Cronk, M.R., O'neill, J.W. and Zhang, K.Y. Crystal structure of E. coli β-carbonic anhydrase, an enzyme with an unusual pH-dependent activity. Protein Sci. 10 (2001) 911–922. [PMID: 11316870]
7.  Merlin, C., Masters, M., McAteer, S. and Coulson, A. Why is carbonic anhydrase essential to Escherichia coli. J. Bacteriol. 185 (2003) 6415–6424. [PMID: 14563877]
[EC 4.2.1.1 created 1961, modified 2016]
 
 
EC 4.2.1.2     
Accepted name: fumarate hydratase
Reaction: (S)-malate = fumarate + H2O
Other name(s): fumarase; L-malate hydro-lyase; (S)-malate hydro-lyase
Systematic name: (S)-malate hydro-lyase (fumarate-forming)
References:
1.  Alberty, R.A. Fumarase. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), The Enzymes, 2nd edn, vol. 5, Academic Press, New York, 1961, pp. 531–544.
2.  Kanarek, L. and Hill, R.L. The preparation and characterization of fumarase from swine heart muscle. J. Biol. Chem. 239 (1964) 4202–4206. [PMID: 14247669]
[EC 4.2.1.2 created 1961]
 
 
EC 4.2.1.3     
Accepted name: aconitate hydratase
Reaction: citrate = isocitrate (overall reaction)
(1a) citrate = cis-aconitate + H2O
(1b) cis-aconitate + H2O = isocitrate
Glossary: isocitrate = (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate (previously known as threo-Ds-isocitrate)
cis-aconitate = (Z)-prop-1-ene-1,2,3-tricarboxylate
Other name(s): cis-aconitase; aconitase; AcnB; 2-methylaconitate hydratase; citrate(isocitrate) hydro-lyase
Systematic name: citrate(isocitrate) hydro-lyase (cis-aconitate-forming)
Comments: Besides interconverting citrate and cis-aconitate, it also interconverts cis-aconitate with isocitrate and, hence, interconverts citrate and isocitrate. The equilibrium mixture is 91% citrate, 6% isocitrate and 3% aconitate. cis-Aconitate is used to designate the isomer (Z)-prop-1-ene-1,2,3-tricarboxylate. An iron-sulfur protein, containing a [4Fe-4S] cluster to which the substrate binds.
References:
1.  Dickman, S.R. Aconitase. In: Boyer, P.D., Lardy, H. and Myrbäck, K (Ed.), The Enzymes, 2nd edn, vol. 5, Academic Press, New York, 1961, pp. 495–510.
2.  Morrison, J.F. The purification of aconitase. Biochem. J. 56 (1954) 99–105. [PMID: 13126098]
3.  Lauble, H., Kennedy, M.C., Beinert, H. and Stout, C.D. Crystal structures of aconitase with trans-aconitate and nitrocitrate bound. J. Mol. Biol. 237 (1994) 437–451. [PMID: 8151704]
[EC 4.2.1.3 created 1961, modified 2003]
 
 
EC 4.2.1.4      
Deleted entry: citrate dehydratase. Now known to be a partial reaction catalysed by EC 4.2.1.3, aconitate hydratase.
[EC 4.2.1.4 created 1961, deleted 2013]
 
 
EC 4.2.1.5     
Accepted name: arabinonate dehydratase
Reaction: D-arabinonate = 2-dehydro-3-deoxy-D-arabinonate + H2O
Other name(s): D-arabinonate hydro-lyase
Systematic name: D-arabinonate hydro-lyase (2-dehydro-3-deoxy-D-arabinonate-forming)
References:
1.  Palleroni, N.J. and Doudoroff, M. Characterization and properties of 2-keto-3-deoxy-D-arabonic acid. J. Biol. Chem. 223 (1956) 499–508. [PMID: 13376619]
[EC 4.2.1.5 created 1961]
 
 
EC 4.2.1.6     
Accepted name: galactonate dehydratase
Reaction: D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O
Other name(s): D-galactonate dehydrase; D-galactonate dehydratase; D-galactonate hydro-lyase
Systematic name: D-galactonate hydro-lyase (2-dehydro-3-deoxy-D-galactonate-forming)
Comments: The enzyme shows no activity with D-gluconate [2]. cf. EC 4.2.1.140, gluconate/galactonate dehydratase.
References:
1.  De Ley, J. and Doudoroff, M. The metabolism of D-galactose in Pseudomonas saccharophila. J. Biol. Chem. 227 (1957) 745–757. [PMID: 13462997]
2.  Donald, A., Sibley, D., Lyons, D.E. and Dahms, A.S. D-Galactonate dehydrase. Purification and properties. J. Biol. Chem. 254 (1979) 2132–2137. [PMID: 422572]
[EC 4.2.1.6 created 1961]
 
 
EC 4.2.1.7     
Accepted name: altronate dehydratase
Reaction: D-altronate = 2-dehydro-3-deoxy-D-gluconate + H2O
Other name(s): D-altronate hydro-lyase
Systematic name: D-altronate hydro-lyase (2-dehydro-3-deoxy-D-gluconate-forming)
References:
1.  Smiley, J.D. and Ashwell, G. Uronic acid metabolism in bacteria. III. Purification and properties of D-altronic acid and D-mannonic acid dehydrases in Escherichia coli. J. Biol. Chem. 235 (1960) 1571–1575. [PMID: 13831814]
[EC 4.2.1.7 created 1961, deleted 1972, reinstated 1976]
 
 
EC 4.2.1.8     
Accepted name: mannonate dehydratase
Reaction: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O
Other name(s): mannonic hydrolase; mannonate hydrolyase; altronic hydro-lyase; altronate hydrolase; D-mannonate hydrolyase; D-mannonate hydro-lyase
Systematic name: D-mannonate hydro-lyase (2-dehydro-3-deoxy-D-gluconate-forming)
References:
1.  Ashwell, G., Wahba, A.J. and Hickman, J. A new pathway of uronic acid metabolism. Biochim. Biophys. Acta 30 (1958) 186–187. [PMID: 13584413]
2.  Robert-Baudouy, J.M. and Stoeber, F.R. [Purification and properties of D-mannonate hydrolyase from Escherichia coli K12] Biochim. Biophys. Acta 309 (1973) 473–485. [PMID: 4581499]
[EC 4.2.1.8 created 1961, modified 1976]
 
 
EC 4.2.1.9     
Accepted name: dihydroxy-acid dehydratase
Reaction: 2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O
Other name(s): acetohydroxyacid dehydratase; α,β-dihydroxyacid dehydratase; 2,3-dihydroxyisovalerate dehydratase; α,β-dihydroxyisovalerate dehydratase; dihydroxy acid dehydrase; DHAD; 2,3-dihydroxy-acid hydro-lyase
Systematic name: 2,3-dihydroxy-3-methylbutanoate hydro-lyase (3-methyl-2-oxobutanoate-forming)
References:
1.  Kanamori, M. and Wixom, R.L. Studies in valine biosynthesis. V. Characteristics of the purified dihydroxyacid dehydratase from spinach leaves. J. Biol. Chem. 238 (1963) 998–1005. [PMID: 13962154]
2.  Myers, J.W. Dihydroxy acid dehydrase: an enzyme involved in the biosynthesis of isoleucine and valine. J. Biol. Chem. 236 (1961) 1414–1418. [PMID: 13727223]
[EC 4.2.1.9 created 1961]
 
 
EC 4.2.1.10     
Accepted name: 3-dehydroquinate dehydratase
Reaction: 3-dehydroquinate = 3-dehydroshikimate + H2O
Glossary: quinate = (1R,3R,4R,5R)-1,3,4,5-tetrahydroxycyclohexanecarboxylic acid and is a cyclitol carboxylate
The numbering system used for the 3-dehydroquinate is that of the recommendations on cyclitols, sections I-8 and I-9: and is shown in the reaction diagram). The use of the term ’5-dehydroquinate’ for this compound is based on an earlier system of numbering.
Other name(s): 3-dehydroquinate hydrolase; DHQase; dehydroquinate dehydratase; 3-dehydroquinase; 5-dehydroquinase; dehydroquinase; 5-dehydroquinate dehydratase; 5-dehydroquinate hydro-lyase; 3-dehydroquinate hydro-lyase
Systematic name: 3-dehydroquinate hydro-lyase (3-dehydroshikimate-forming)
References:
1.  Mitsuhashi, S. and Davis, B.D. Aromatic biosynthesis. XII. Conversion of 5-dehydroquinic acid to 5-dehydroshikimic acid by 5-dehydroquinase. Biochim. Biophys. Acta 15 (1954) 54–61. [PMID: 13198937]
2.  Mitsuhashi, S. and Davis, B.D. Aromatic biosynthesis. XIII. Conversion of quinic acid to 5-dehydroquinic acid by quinic dehydrogenase. Biochim. Biophys. Acta 15 (1954) 268–280. [PMID: 13208693]
[EC 4.2.1.10 created 1961, modified 1976]
 
 
EC 4.2.1.11     
Accepted name: phosphopyruvate hydratase
Reaction: 2-phospho-D-glycerate = phosphoenolpyruvate + H2O
Other name(s): enolase; 2-phosphoglycerate dehydratase; 14-3-2-protein; nervous-system specific enolase; phosphoenolpyruvate hydratase; 2-phosphoglycerate dehydratase; 2-phosphoglyceric dehydratase; 2-phosphoglycerate enolase; γ-enolase; 2-phospho-D-glycerate hydro-lyase
Systematic name: 2-phospho-D-glycerate hydro-lyase (phosphoenolpyruvate-forming)
Comments: Also acts on 3-phospho-D-erythronate.
References:
1.  Holt, A. and Wold, F. The isolation and characterization of rabbit muscle enolase. J. Biol. Chem. 236 (1961) 3227–3231. [PMID: 13908561]
2.  Malmström, B.G. Enolase. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), The Enzymes, 2nd edn, vol. 5, Academic Press, New York, 1961, pp. 471–494.
3.  Westhead, E.W. and McLain, G. Purification of brewers’ and bakers’ yeast enolase yielding a single active component. J. Biol. Chem. 239 (1964) 2464–2468. [PMID: 14235523]
[EC 4.2.1.11 created 1961]
 
 
EC 4.2.1.12     
Accepted name: phosphogluconate dehydratase
Reaction: 6-phospho-D-gluconate = 2-dehydro-3-deoxy-6-phospho-D-gluconate + H2O
Other name(s): 6-phosphogluconate dehydratase; 6-phosphogluconic dehydrase; gluconate-6-phosphate dehydratase; gluconate 6-phosphate dehydratase; 6-phosphogluconate dehydrase; 6-phospho-D-gluconate hydro-lyase
Systematic name: 6-phospho-D-gluconate hydro-lyase (2-dehydro-3-deoxy-6-phospho-D-gluconate-forming)
References:
1.  Meloche, H.P. and Wood, W.A. The mechanism of 6-phosphogluconic dehydrase. J. Biol. Chem. 239 (1964) 3505–3510. [PMID: 14245409]
[EC 4.2.1.12 created 1961]
 
 
EC 4.2.1.13      
Transferred entry: L-serine dehydratase. Now EC 4.3.1.17, L-serine ammonia-lyase
[EC 4.2.1.13 created 1961, deleted 2001]
 
 
EC 4.2.1.14      
Transferred entry: D-serine dehydratase. Now EC 4.3.1.18, D-serine ammonia-lyase
[EC 4.2.1.14 created 1961, deleted 2001]
 
 
EC 4.2.1.15      
Deleted entry:  homoserine dehydratase. Identical with EC 4.4.1.1 cystathionine γ-lyase
[EC 4.2.1.15 created 1961, deleted 1972]
 
 
EC 4.2.1.16      
Transferred entry: threonine dehydratase. Now EC 4.3.1.19, threonine ammonia-lyase
[EC 4.2.1.16 created 1961, deleted 2001]
 
 
EC 4.2.1.17     
Accepted name: enoyl-CoA hydratase
Reaction: (3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H2O
Other name(s): enoyl hydrase; unsaturated acyl-CoA hydratase; β-hydroxyacyl-CoA dehydrase; β-hydroxyacid dehydrase; acyl coenzyme A hydrase; crotonase; crotonyl hydrase; 2-octenoyl coenzyme A hydrase; enoyl coenzyme A hydratase; 2-enoyl-CoA hydratase; short-chain enoyl-CoA hydratase; ECH; trans-2-enoyl-CoA hydratase; enoyl coenzyme A hydrase (D); enoyl coenzyme A hydrase (L); short chain enoyl coenzyme A hydratase; D-3-hydroxyacyl-CoA dehydratase; enol-CoA hydratase
Systematic name: (3S)-3-hydroxyacyl-CoA hydro-lyase
Comments: Acts in the reverse direction. With cis-compounds, yields (3R)-3-hydroxyacyl-CoA. cf. EC 4.2.1.74 long-chain-enoyl-CoA hydratase.
References:
1.  Moskowitz, G.J. and Merrick, J.M. Metabolism of poly-β-hydroxybutyrate. II. Enzymatic synthesis of D-(-)-β-hydroxybutyryl coenzyme A by an enoyl hydrase from Rhodospirillum rubrum. Biochemistry 8 (1969) 2748–2755. [PMID: 5808333]
2.  Stern, J.R. Thioltranscrotylase and β-hydroxybutyryl CoA racemase activities of crystalline crotonase. Biochim. Biophys. Acta 26 (1957) 641–643. [PMID: 13499425]
[EC 4.2.1.17 created 1961]
 
 
EC 4.2.1.18     
Accepted name: methylglutaconyl-CoA hydratase
Reaction: (S)-3-hydroxy-3-methylglutaryl-CoA = trans-3-methylglutaconyl-CoA + H2O
Other name(s): methylglutaconyl coenzyme A hydratase; 3-methylglutaconyl CoA hydratase; methylglutaconase; (S)-3-hydroxy-3-methylglutaryl-CoA hydro-lyase
Systematic name: (S)-3-hydroxy-3-methylglutaryl-CoA hydro-lyase (trans-3-methylglutaconyl-CoA-forming)
References:
1.  Hilz, H., Knappe, J., Ringelmann, E. and Lynen, F. Methylglutaconase, eine neue Hydratase, die am Stoffwechsel verzweigter Carbonsäuren beteiligt ist. Biochem. Z. 329 (1958) 476–489. [PMID: 13535602]
[EC 4.2.1.18 created 1961]
 
 
EC 4.2.1.19     
Accepted name: imidazoleglycerol-phosphate dehydratase
Reaction: D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H2O
Other name(s): IGP dehydratase; D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate hydro-lyase
Systematic name: D-erythro-1-(imidazol-4-yl)glycerol-3-phosphate hydro-lyase [3-(imidazol-4-yl)-2-oxopropyl-phosphate-forming]
References:
1.  Ames, B.N. The biosynthesis of histidine: D-erythro-Imidazoleglycerol phosphate dehydrase. J. Biol. Chem. 228 (1957) 131–143. [PMID: 13475302]
[EC 4.2.1.19 created 1961]
 
 
EC 4.2.1.20     
Accepted name: tryptophan synthase
Reaction: L-serine + 1-C-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + D-glyceraldehyde 3-phosphate + H2O (overall reaction)
(1a) 1-C-(indol-3-yl)glycerol 3-phosphate = indole + D-glyceraldehyde 3-phosphate
(1b) L-serine + indole = L-tryptophan + H2O
Other name(s): L-tryptophan synthetase; indoleglycerol phosphate aldolase; tryptophan desmolase; tryptophan synthetase; L-serine hydro-lyase (adding indoleglycerol-phosphate); L-serine hydro-lyase [adding 1-C-(indol-3-yl)glycerol 3-phosphate, L-tryptophan and glyceraldehyde-3-phosphate-forming]
Systematic name: L-serine hydro-lyase [adding 1-C-(indol-3-yl)glycerol 3-phosphate, L-tryptophan and D-glyceraldehyde-3-phosphate-forming]
Comments: A pyridoxal-phosphate protein. The α-subunit catalyses the conversion of 1-C-(indol-3-yl)glycerol 3-phosphate to indole and D-glyceraldehyde 3-phosphate (this reaction was included formerly under EC 4.1.2.8). The indole migrates to the β-subunit where, in the presence of pyridoxal 5′-phosphate, it is combined with L-serine to form L-tryptophan. In some organisms this enzyme is part of a multifunctional protein that also includes one or more of the enzymes EC 2.4.2.18 (anthranilate phosphoribosyltransferase), EC 4.1.1.48 (indole-3-glycerol-phosphate synthase), EC 4.1.3.27 (anthranilate synthase) and EC 5.3.1.24 (phosphoribosylanthranilate isomerase). In thermophilic organisms, where the high temperature enhances diffusion and causes the loss of indole, a protein similar to the β subunit can be found (EC 4.2.1.122). That enzyme cannot combine with the α unit of EC 4.2.1.20 to form a complex.
References:
1.  Crawford, I.P. and Yanofsky, C. On the separation of the tryptophan synthetase of Escherichia coli into two protein components. Proc. Natl. Acad. Sci. USA 44 (1958) 1161–1170. [PMID: 16590328]
2.  Creighton, T.E. and Yanofsky, C. Chorismate to tryptophan (Escherichia coli) - anthranilate synthetase, PR transferase, PRA isomerase, InGP synthetase, tryptophan synthetase. Methods Enzymol. 17A (1970) 365–380.
3.  Hütter, R., Niederberger, P. and DeMoss, J.A. Tryptophan synthetic genes in eukaryotic microorganisms. Annu. Rev. Microbiol. 40 (1986) 55–77. [PMID: 3535653]
4.  Hyde, C.C., Ahmed, S.A., Padlan, E.A., Miles, E.W. and Davies, D.R. Three-dimensional structure of the tryptophan synthase α2β2 multienzyme complex from Salmonella typhimurium. J. Biol. Chem. 263 (1988) 17857–17871. [PMID: 3053720]
5.  Woehl, E. and Dunn, M.F. Mechanisms of monovalent cation action in enzyme catalysis: the tryptophan synthase α-, β-, and αβ-reactions. Biochemistry 38 (1999) 7131–7141. [PMID: 10353823]
[EC 4.2.1.20 created 1961, modified 1976, modified 2002, modified 2011]
 
 
EC 4.2.1.21      
Deleted entry:  cystathionine β-synthase. Now EC 4.2.1.22 cystathionine β-synthase
[EC 4.2.1.21 created 1961, deleted 1964]
 
 
EC 4.2.1.22     
Accepted name: cystathionine β-synthase
Reaction: L-serine + L-homocysteine = L-cystathionine + H2O
Other name(s): serine sulfhydrase; β-thionase; methylcysteine synthase; cysteine synthase (incorrect); serine sulfhydrylase; L-serine hydro-lyase (adding homocysteine)
Systematic name: L-serine hydro-lyase (adding homocysteine; L-cystathionine-forming)
Comments: A pyridoxal-phosphate protein. A multifunctional enzyme: catalyses β-replacement reactions between L-serine, L-cysteine, cysteine thioethers, or some other β-substituted α-L-amino acids, and a variety of mercaptans.
References:
1.  Braunstein, A.E., Goryachinkova, E.V., Tolosa, E.A., Willhardt, I.H. and Yefremova, L.L. Specificity and some other properties of liver serine sulphhydrase: evidence for its identity with cystathionine-synthase. Biochim. Biophys. Acta. 242 (1971) 247–260. [PMID: 5121611]
2.  Nakagawa, H. and Kimura, H. Purification and properties of cystathionine synthetase synthetase from rat liver: separation of cystathionine synthetase from serine dehydratase. Biochem. Biophys. Res. Commun. 32 (1968) 209–214. [PMID: 5672136]
3.  Schlossmann, K., Brüggemann, J. and Lynen, F. Biosynthese des Cysteins. I. Nachweis und Isolierung der Serinsulfhydrase aus Bäckerhefe. Biochem. Z. 336 (1962) 258–273. [PMID: 13991884]
[EC 4.2.1.22 created 1961 (EC 4.2.1.21 created 1961, incorporated 1964, EC 4.2.1.23 created 1961, incorporated 1972)]
 
 
EC 4.2.1.23      
Deleted entry:  methylcysteine synthase. The reaction was due to a side-reaction of EC 4.2.1.22 cystathionine β-synthase
[EC 4.2.1.23 created 1961, deleted 1972]
 
 
EC 4.2.1.24     
Accepted name: porphobilinogen synthase
Reaction: 2 5-aminolevulinate = porphobilinogen + 2 H2O
Glossary: 5-aminolevulinate = δ-aminolevulinate
Other name(s): aminolevulinate dehydratase; δ-aminolevulinate dehydratase; δ-aminolevulinic acid dehydrase; δ-aminolevulinic acid dehydratase; aminolevulinic dehydratase; δ-aminolevulinic dehydratase; 5-levulinic acid dehydratase; 5-aminolevulinate hydro-lyase (adding 5-aminolevulinate and cyclizing); hemB (gene name)
Systematic name: 5-aminolevulinate hydro-lyase (adding 5-aminolevulinate and cyclizing; porphobilinogen-forming)
Comments: The enzyme catalyses the asymmetric condensation and cyclization of two 5-aminolevulinate molecules, which is the first common step in the biosynthesis of tetrapyrrole pigments such as porphyrin, chlorophyll, vitamin B12, siroheme, phycobilin, and cofactor F430. The enzyme is widespread, being essential in organisms that carry out respiration, photosynthesis, or methanogenesis. The enzymes from most organisms utilize metal ions (Zn2+, Mg2+, K+, and Na+) as cofactors that reside at multiple sites, including the active site and allosteric sites. Enzymes from archaea, yeast, and metazoa (including human) contain Zn2+ at the active site. In humans, the enzyme is a primary target for the environmental toxin Pb. The enzymes from some organisms utilize a dynamic equilibrium between architecturally distinct multimeric assemblies as a means for allosteric regulation.
References:
1.  Gibson, K.D., Neuberger, A. and Scott, J.J. The purification and properties of δ-aminolaevulic acid dehydrase. Biochem. J. 61 (1955) 618–629. [PMID: 13276347]
2.  Komai, H. and Neilands, J.B. The metalloprotein nature of Ustilago δ-aminolevulinate dehydratase. Biochim. Biophys. Acta 171 (1969) 311–320. [PMID: 5773436]
3.  Yamasaki, H. and Moriyama, T. δ-Aminolevulinic acid dehydratase of Mycobacterium phlei. Biochim. Biophys. Acta 227 (1971) 698–705. [PMID: 4998716]
4.  Mitchell, L.W. and Jaffe, E.K. Porphobilinogen synthase from Escherichia coli is a Zn(II) metalloenzyme stimulated by Mg(II). Arch. Biochem. Biophys. 300 (1993) 169–177. [PMID: 8424649]
5.  Jaffe, E.K., Ali, S., Mitchell, L.W., Taylor, K.M., Volin, M. and Markham, G.D. Characterization of the role of the stimulatory magnesium of Escherichia coli porphobilinogen synthase. Biochemistry 34 (1995) 244–251. [PMID: 7819203]
6.  Warren, M.J., Cooper, J.B., Wood, S.P. and Shoolingin-Jordan, P.M. Lead poisoning, haem synthesis and 5-aminolaevulinic acid dehydratase. Trends Biochem. Sci. 23 (1998) 217–221. [PMID: 9644976]
7.  Jaffe, E.K. and Lawrence, S.H. Allostery and the dynamic oligomerization of porphobilinogen synthase. Arch. Biochem. Biophys. 519 (2012) 144–153. [PMID: 22037356]
8.  Tian, B.X., Erdtman, E. and Eriksson, L.A. Catalytic mechanism of porphobilinogen synthase: the chemical step revisited by QM/MM calculations. J. Phys. Chem. B 116 (2012) 12105–12112. [PMID: 22974111]
[EC 4.2.1.24 created 1961]
 
 
EC 4.2.1.25     
Accepted name: L-arabinonate dehydratase
Reaction: L-arabinonate = 2-dehydro-3-deoxy-L-arabinonate + H2O
Other name(s): L-arabonate dehydrase; L-arabonate dehydratase; L-arabinonate hydro-lyase
Systematic name: L-arabinonate hydro-lyase (2-dehydro-3-deoxy-L-arabinonate-forming)
References:
1.  Weimberg, R. L-2-Keto-4,5-dihydroxyvaleric acid: an intermediate in the oxidation of L-arabinose by Pseudomonase saccharophila. J. Biol. Chem. 234 (1959) 727–732. [PMID: 13654251]
[EC 4.2.1.25 created 1965]
 
 
EC 4.2.1.26      
Deleted entry: aminodeoxygluconate dehydratase. This enzyme was transferred to EC 4.3.1.21, aminodeoxygluconate ammonia-lyase, which has since been deleted. The enzyme is identical to EC 4.3.1.9, glucosaminate ammonia-lyase
[EC 4.2.1.26 created 1965, deleted 2002]
 
 
EC 4.2.1.27     
Accepted name: acetylenecarboxylate hydratase
Reaction: 3-oxopropanoate = propynoate + H2O
Other name(s): acetylenemonocarboxylate hydratase; alkynoate hydratase; acetylenemonocarboxylate hydrase; acetylenemonocarboxylic acid hydrase; malonate-semialdehyde dehydratase; 3-oxopropanoate hydro-lyase
Systematic name: 3-oxopropanoate hydro-lyase (propynoate-forming)
Comments: The reaction is effectively irreversible, favouring oxopropanoate (malonic semialdehyde) and its tautomers. Also acts on but-3-ynoate forming acetoacetate. The mechanism appears to involve hydration of the acetylene to 3-hydroxypropenoate, which will spontaneously tautomerize to 3-oxopropanoate. It is thus analogous to EC 4.1.1.78, acetylenedicarboxylate decarboxylase, in its mechanism.
References:
1.  Van den Tweel, W.J.J. and De Bont, J.A.M. Metabolism of 3-butyn-1-ol by Pseudomonas BB1. J. Gen. Microbiol. 131 (1985) 3155–3162.
2.  Yamada, E.W. and Jakoby, W.B. Enzymatic utilization of acetylenic compounds. II. Acetylenemonocarboxylic acid hydrase. J. Biol. Chem. 234 (1959) 941–945. [PMID: 13654296]
[EC 4.2.1.27 created 1965, (EC 4.2.1.71 created 1978, modified 1989, modified 2000, incorporated 2004) modified 2004]
 
 
EC 4.2.1.28     
Accepted name: propanediol dehydratase
Reaction: propane-1,2-diol = propanal + H2O
Other name(s): meso-2,3-butanediol dehydrase; diol dehydratase; DL-1,2-propanediol hydro-lyase; diol dehydrase; adenosylcobalamin-dependent diol dehydratase; propanediol dehydrase; coenzyme B12-dependent diol dehydrase; 1,2-propanediol dehydratase; dioldehydratase; propane-1,2-diol hydro-lyase; RiDD
Systematic name: propane-1,2-diol hydro-lyase (propanal-forming)
Comments: Two different forms of the enzyme have been described. One form requires a cobamide coenzyme, while the other is a glycyl radical enzyme. The cobamide-dependent enzyme has been shown to also dehydrate ethylene glycol to acetaldehyde.
References:
1.  Abeles, R.H. and Lee, H.A., Jr. An intramolecular oxidation-reduction requiring a cobamide coenzyme. J. Biol. Chem. 236 (1961) 2347–2350. [PMID: 13680987]
2.  Lee, H.A. and Abeles, R.H. Purification and properties of dioldehydrase, and enzyme requiring a cobamide coenzyme. J. Biol. Chem. 238 (1963) 2367–2373. [PMID: 13929077]
3.  Forage, R.G. and Foster, M.A. Glycerol fermentation in Klebsiella pneumoniae: functions of the coenzyme B12-dependent glycerol and diol dehydratases. J. Bacteriol. 149 (1982) 413–419. [PMID: 7035429]
4.  LaMattina, J.W., Keul, N.D., Reitzer, P., Kapoor, S., Galzerani, F., Koch, D.J., Gouvea, I.E. and Lanzilotta, W.N. 1,2-Propanediol dehydration in Roseburia inulinivorans: structural basis for substrate and enantiomer selectivity. J. Biol. Chem. 291 (2016) 15515–15526. [PMID: 27252380]
[EC 4.2.1.28 created 1965]
 
 
EC 4.2.1.29      
Transferred entry: indoleacetaldoxime dehydratase. Now EC 4.99.1.6, indoleacetaldoxime dehydratase. The enzyme was classified incorrectly as a C-O lyase when the bond broken is a N-O bond
[EC 4.2.1.29 created 1965, deleted 2004]
 
 
EC 4.2.1.30     
Accepted name: glycerol dehydratase
Reaction: glycerol = 3-hydroxypropanal + H2O
Other name(s): glycerol dehydrase; glycerol hydro-lyase; dhaB (gene name)
Systematic name: glycerol hydro-lyase (3-hydroxypropanal-forming)
Comments: Two different forms of the enzyme have been described. One form requires a cobamide coenzyme, while the other is a glycyl radical enzyme.
References:
1.  Smiley, K.L. and Sobolov, M. A cobamide-requiring glycerol dehydrase from an acrolein-forming Lactobacillus. Arch. Biochem. Biophys. 97 (1962) 538–543. [PMID: 14039344]
2.  Schneider, Z. and Pawelkiewicz, J. The properties of glycerol dehydratase isolated from Aerobacter aerogenes, and the properties of the apoenzyme subunits. Acta Biochim. Pol. 13 (1966) 311–328. [PMID: 5962440]
3.  Schneider, Z., Larsen, E.G., Jacobsen, G., Johnson, B.C. and Pawelkiewicz, J. Purification and properties of glycerol dehydrase. J. Biol. Chem. 245 (1970) 3388–3396. [PMID: 4989992]
4.  Forage, R.G. and Foster, M.A. Glycerol fermentation in Klebsiella pneumoniae: functions of the coenzyme B12-dependent glycerol and diol dehydratases. J. Bacteriol. 149 (1982) 413–419. [PMID: 7035429]
5.  O'Brien, J.R., Raynaud, C., Croux, C., Girbal, L., Soucaille, P. and Lanzilotta, W.N. Insight into the mechanism of the B12-independent glycerol dehydratase from Clostridium butyricum: preliminary biochemical and structural characterization. Biochemistry 43 (2004) 4635–4645. [PMID: 15096031]
[EC 4.2.1.30 created 1972]
 
 
EC 4.2.1.31     
Accepted name: maleate hydratase
Reaction: (R)-malate = maleate + H2O
Other name(s): D-malate hydro-lyase; malease; (R)-malate hydro-lyase
Systematic name: (R)-malate hydro-lyase (maleate-forming)
References:
1.  Britten, J.S., Morell, H. and Taggart, J.V. Anion activation of maleate hydratase. Biochim. Biophys. Acta 185 (1969) 220–227. [PMID: 5796106]
2.  Sacks, W. and Jensen, C.O. Malease, a hydrase from corn kernals. J. Biol. Chem. 192 (1951) 231–236. [PMID: 14917669]
[EC 4.2.1.31 created 1972]
 
 
EC 4.2.1.32     
Accepted name: L(+)-tartrate dehydratase
Reaction: (R,R)-tartrate = oxaloacetate + H2O
Other name(s): tartrate dehydratase; tartaric acid dehydrase; L-tartrate dehydratase; L-(+)-tartaric acid dehydratase; (R,R)-tartrate hydro-lyase
Systematic name: (R,R)-tartrate hydro-lyase (oxaloacetate-forming)
Comments: The enzyme exists in an inactive low-molecular-mass form, which is converted into active enzyme in the presence of Fe2+ and thiol. cf. EC 4.2.1.81 D(-)-tartrate dehydratase.
References:
1.  Hurlbert, R.E. and Jakoby, W.B. Tartaric acid metabolism. I. Subunits of L(+)-tartaric acid dehydrase. J. Biol. Chem. 240 (1965) 2772–2777. [PMID: 14342293]
[EC 4.2.1.32 created 1972, modified 1986]
 
 
EC 4.2.1.33     
Accepted name: 3-isopropylmalate dehydratase
Reaction: (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate (overall reaction)
(1a) (2R,3S)-3-isopropylmalate = 2-isopropylmaleate + H2O
(1b) 2-isopropylmaleate + H2O = (2S)-2-isopropylmalate
Glossary: α-isopropylmalate = (2S)-2-isopropylmalate
β-isopropylmalate = (2R,3S)-3-isopropylmalate
Other name(s): (2R,3S)-3-isopropylmalate hydro-lyase; β-isopropylmalate dehydratase; isopropylmalate isomerase; α-isopropylmalate isomerase; 3-isopropylmalate hydro-lyase
Systematic name: (2R,3S)-3-isopropylmalate hydro-lyase (2-isopropylmaleate-forming)
Comments: Forms part of the leucine biosynthesis pathway. The enzyme brings about the interconversion of the two isomers of isopropylmalate. It contains an iron-sulfur cluster.
References:
1.  Gross, S.R., Burns, R.O. and Umbarger, H.E. The biosynthesis of leucine. II. The enzymic isomerization of β-carboxy-β-hydroxyisocaproate and α-hydroxy-β-carboxyisocaproate. Biochemistry 2 (1963) 1046–1052. [PMID: 14087357]
2.  Calvo, J. M., Stevens, C. M., Kalyanpur, M. G., and Umbarger, H. E. The absolute configuration of α-hydroxy-β-carboxyisocaproic acid (3-isopropylmalic acid), an intermediate in leucine biosynthesis. Biochemistry 3 (1964) 2024–2027. [PMID: 14269331]
3.  Cole, F.E., Kalyanpur, M. G. and Stevens, C. M. Absolute configuration of α-isopropylmalate and the mechanism of its conversion to β-isopropylmalate in the biosynthesis of leucine. Biochemistry 12 (1973) 3346–3350. [PMID: 4270046]
4.  Jang, S. and Imlay, J.A. Micromolar intracellular hydrogen peroxide disrupts metabolism by damaging iron-sulfur enzymes. J. Biol. Chem. 282 (2007) 929–937. [PMID: 17102132]
[EC 4.2.1.33 created 1972, modified 1976, modified 2012]
 
 
EC 4.2.1.34     
Accepted name: (S)-2-methylmalate dehydratase
Reaction: (S)-2-methylmalate = 2-methylfumarate + H2O
Other name(s): mesaconate hydratase; (+)-citramalate hydro-lyase; L-citramalate hydrolase; citramalate dehydratase; (+)-citramalic hydro-lyase; mesaconate mesaconase; mesaconase; (S)-2-methylmalate hydro-lyase
Systematic name: (S)-2-methylmalate hydro-lyase (2-methylfumarate-forming)
Comments: Also hydrates fumarate to (S)-malate.
References:
1.  Blair, A.H. and Barker, H.A. Assay and purification of (+)-citramalate hydro-lyase components from Clostridium tetanomorphum. J. Biol. Chem. 241 (1966) 400–408. [PMID: 5903732]
2.  Wang, C.C. and Barker, H.A. Purification and properties of L-citramalate hydrolyase. J. Biol. Chem. 244 (1969) 2516–2526. [PMID: 5769987]
[EC 4.2.1.34 created 1972]
 
 
EC 4.2.1.35     
Accepted name: (R)-2-methylmalate dehydratase
Reaction: (R)-2-methylmalate = 2-methylmaleate + H2O
Other name(s): citraconate hydratase; citraconase; citramalate hydro-lyase; (-)-citramalate hydro-lyase; (R)-2-methylmalate hydro-lyase
Systematic name: (R)-2-methylmalate hydro-lyase (2-methylmaleate-forming)
Comments: Requires Fe2+.
References:
1.  Subramanian, S.S. and Raghavendra Rao, M.R. Purification and properties of citraconase. J. Biol. Chem. 243 (1968) 2367–2372. [PMID: 4296839]
2.  Raghavendra Rao, M.R., Subramanian, S.S., Rahatekar, H.I. and Paranjape, S.V. Enzymatic hydration of citraconate to (-)citramalate. Biochem. Biophys. Res. Commun. 12 (1963) 78–82. [PMID: 13973053]
[EC 4.2.1.35 created 1972]
 
 
EC 4.2.1.36     
Accepted name: homoaconitate hydratase
Reaction: (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate = (Z)-but-1-ene-1,2,4-tricarboxylate + H2O
Glossary: cis-homoaconitate = (Z)-but-1-ene-1,2,4-tricarboxylate
(R)-homocitrate = (2R)-2-hydroxybutane-1,2,4-tricarboxylate
homoisocitrate = (-)-threo-homoisocitrate = (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate
Other name(s): homoaconitase; cis-homoaconitase; HACN; Lys4; LysF; 2-hydroxybutane-1,2,4-tricarboxylate hydro-lyase (incorrect)
Systematic name: (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate hydro-lyase [(Z)-but-1-ene-1,2,4-tricarboxylate-forming]
Comments: Requires a [4Fe-4S] cluster for activity. The enzyme from the hyperthermophilic eubacterium Thermus thermophilus can catalyse the reaction shown above but cannot catalyse the previously described reaction, i.e. formation of (R)-homocitrate by hydration of cis-homoaconitate. The enzyme responsible for the conversion of cis-homoaconitate into (R)-homocitrate in T. thermophilus is unknown at present but the reaction can be catalysed in vitro using aconitate hydratase from pig (EC 4.2.1.3) [2].
References:
1.  Strassman, M. and Ceci, L.N. Enzymatic formation of cis-homoaconitic acid, an intermediate in lysine biosynthesis in yeast. J. Biol. Chem. 241 (1966) 5401–5407. [PMID: 5954805]
2.  Jia, Y., Tomita, T., Yamauchi, K., Nishiyama, M. and Palmer, D.R. Kinetics and product analysis of the reaction catalysed by recombinant homoaconitase from Thermus thermophilus. Biochem. J. 396 (2006) 479–485. [PMID: 16524361]
3.  Zabriskie, T.M. and Jackson, M.D. Lysine biosynthesis and metabolism in fungi. Nat. Prod. Rep. 17 (2000) 85–97. [PMID: 10714900]
[EC 4.2.1.36 created 1972, modified 2007]
 
 
EC 4.2.1.37      
Transferred entry: trans-epoxysuccinate hydratase. Now EC 3.3.2.4, trans-epoxysuccinate hydrolase
[EC 4.2.1.37 created 1972, deleted 1992]
 
 
EC 4.2.1.38      
Transferred entry: erythro-3-hydroxyaspartate dehydratase. Now EC 4.3.1.20, erythro-3-hydroxyaspartate ammonia-lyase
[EC 4.2.1.38 created 1972, deleted 2001]
 
 
EC 4.2.1.39     
Accepted name: gluconate dehydratase
Reaction: D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O
Other name(s): D-gluconate dehydratase; D-gluconate hydro-lyase
Systematic name: D-gluconate hydro-lyase (2-dehydro-3-deoxy-D-gluconate-forming)
Comments: The enzyme shows no activity with D-galactonate [2]. cf. EC 4.2.1.140, gluconate/galactonate dehydratase.
References:
1.  Andreesen, J.R. and Gottschalk, G. The occurrence of a modified Entner-Doudoroff pathway in Clostridium aceticum. Arch. Mikrobiol. 69 (1969) 160–170. [PMID: 5383859]
2.  Bender, R. and Gottschalk, G. Purification and properties of D-gluconate dehydratase from Clostridium pasteurianum. Eur. J. Biochem. 40 (1973) 309–321. [PMID: 4772682]
[EC 4.2.1.39 created 1972]
 
 
EC 4.2.1.40     
Accepted name: glucarate dehydratase
Reaction: D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H2O
Other name(s): D-glucarate dehydratase; D-glucarate hydro-lyase
Systematic name: D-glucarate hydro-lyase (5-dehydro-4-deoxy-D-glucarate-forming)
References:
1.  Blumenthal, H.J. D-Glucarate dehydrase. Methods Enzymol. 9 (1966) 660–665.
[EC 4.2.1.40 created 1972]
 
 
EC 4.2.1.41     
Accepted name: 5-dehydro-4-deoxyglucarate dehydratase
Reaction: 5-dehydro-4-deoxy-D-glucarate = 2,5-dioxopentanoate + H2O + CO2
Other name(s): 5-keto-4-deoxy-glucarate dehydratase; 5-keto-4-deoxy-glucarate dehydratase; deoxyketoglucarate dehydratase; D-4-deoxy-5-ketoglucarate hydro-lyase; 5-dehydro-4-deoxy-D-glucarate hydro-lyase (decarboxylating)
Systematic name: 5-dehydro-4-deoxy-D-glucarate hydro-lyase (decarboxylating; 2,5-dioxopentanoate-forming)
References:
1.  Jeffcoat, R., Hassall, H. and Dagley, S. Purification and properties of D-4-deoxy-5-oxoglucarate hydro-lyase (decarboxylating). Biochem. J. 115 (1969) 977–983. [PMID: 4982840]
[EC 4.2.1.41 created 1972]
 
 
EC 4.2.1.42     
Accepted name: galactarate dehydratase
Reaction: galactarate = (2R,3S)-2,3-dihydroxy-5-oxohexanedioate + H2O
Glossary: galactarate = (2R,3S,4R,5S)-2,3,4,5-tetrahydroxyhexanedioate
(2R,3S)-2,3-dihydroxy-5-oxohexanedioate = 3-deoxy-L-threo-hex-2-ulosarate
Other name(s): D-galactarate hydro-lyase; D-galactarate hydro-lyase (5-dehydro-4-deoxy-D-glucarate-forming); talrD (gene name)/galrD (gene name); galactarate dehydratase (L-threo-forming)
Systematic name: galactarate hydro-lyase (5-dehydro-4-deoxy-D-glucarate-forming)
Comments: The enzyme from the bacterium Escherichia coli is specific for galactarate [2], while the enzyme from Salmonella typhimurium also has activity with L-talarate (cf. EC 4.2.1.156, L-talarate dehydratase) [3]. cf. EC 4.2.1.158, galactarate dehydratase (D-threo-forming).
References:
1.  Blumenthal, H.J. and Jepson, T. Galactarate dehydrase. Methods Enzymol. 9 (1966) 665–669.
2.  Hubbard, B.K., Koch, M., Palmer, D.R., Babbitt, P.C. and Gerlt, J.A. Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli. Biochemistry 37 (1998) 14369–14375. [PMID: 9772162]
3.  Yew, W.S., Fedorov, A.A., Fedorov, E.V., Almo, S.C. and Gerlt, J.A. Evolution of enzymatic activities in the enolase superfamily: L-talarate/galactarate dehydratase from Salmonella typhimurium LT2. Biochemistry 46 (2007) 9564–9577. [PMID: 17649980]
4.  Rakus, J.F., Kalyanaraman, C., Fedorov, A.A., Fedorov, E.V., Mills-Groninger, F.P., Toro, R., Bonanno, J., Bain, K., Sauder, J.M., Burley, S.K., Almo, S.C., Jacobson, M.P. and Gerlt, J.A. Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis. Biochemistry 48 (2009) 11546–11558. [PMID: 19883118]
[EC 4.2.1.42 created 1972, modified 2015]
 
 
EC 4.2.1.43     
Accepted name: 2-dehydro-3-deoxy-L-arabinonate dehydratase
Reaction: 2-dehydro-3-deoxy-L-arabinonate = 2,5-dioxopentanoate + H2O
Other name(s): 2-keto-3-deoxy-L-arabinonate dehydratase; 2-dehydro-3-deoxy-L-arabinonate hydro-lyase
Systematic name: 2-dehydro-3-deoxy-L-arabinonate hydro-lyase (2,5-dioxopentanoate-forming)
References:
1.  Stoolmiller, A.C. and Abeles, R.H. Formation of α-ketoglutaric semialdehyde from L-2-keto-3-deoxyarabonic acid and isolation of L-2-keto-3-deoxyarabonate dehydratase from Pseudomonas saccharophila. J. Biol. Chem. 241 (1966) 5764–5771. [PMID: 5954356]
[EC 4.2.1.43 created 1972]
 
 
EC 4.2.1.44     
Accepted name: myo-inosose-2 dehydratase
Reaction: 2,4,6/3,5-pentahydroxycyclohexanone = 3,5/4-trihydroxycyclohexa-1,2-dione + H2O
Other name(s): inosose 2,3-dehydratase; ketoinositol dehydratase; 2,4,6/3,5-pentahydroxycyclohexanone hydro-lyase
Systematic name: 2,4,6/3,5-pentahydroxycyclohexanone hydro-lyase (3,5/4-trihydroxycyclohexa-1,2-dione-forming)
Comments: Requires Co2+ or Mn2+.
References:
1.  Berman, T. and Magasanik, B. The pathway of myo-inositol degradation in Aerobacter aerogenes. Dehydrogenation and dehydration. J. Biol. Chem. 241 (1966) 800–806. [PMID: 5905122]
[EC 4.2.1.44 created 1972]
 
 
EC 4.2.1.45     
Accepted name: CDP-glucose 4,6-dehydratase
Reaction: CDP-glucose = CDP-4-dehydro-6-deoxy-D-glucose + H2O
Other name(s): cytidine diphosphoglucose oxidoreductase; CDP-glucose 4,6-hydro-lyase
Systematic name: CDP-glucose 4,6-hydro-lyase (CDP-4-dehydro-6-deoxy-D-glucose-forming)
Comments: Requires bound NAD+.
References:
1.  Hey, A.E. and Elbein, A.D. Biosynthesis of tyvelose. The purification and properties of cytidine diphosphate D-glucose oxidoreductase. J. Biol. Chem. 241 (1966) 5473–5478. [PMID: 4380946]
2.  Matsuhashi, S., Matsuhashi, M., Brown, J.G. and Strominger, J.L. Enzymatic synthesis of cytidine diphosphate 3,6-dideoxyhexoses. 3. Cytidine diphosphate D-glucose oxidoreductase. J. Biol. Chem. 241 (1966) 4283–4287. [PMID: 4288651]
3.  Melo, A., Elliott, H. and Glaser, L. The mechanism of 6-deoxyhexose synthesis. I. Intramolecular hydrogen transfer catalyzed by deoxythymidine diphosphate D-glucose oxidoreductase. J. Biol. Chem. 243 (1968) 1467–1474. [PMID: 4869560]
[EC 4.2.1.45 created 1972]
 
 
EC 4.2.1.46     
Accepted name: dTDP-glucose 4,6-dehydratase
Reaction: dTDP-α-D-glucose = dTDP-4-dehydro-6-deoxy-α-D-glucose + H2O
Other name(s): thymidine diphosphoglucose oxidoreductase; TDP-glucose oxidoreductase; dTDP-glucose 4,6-hydro-lyase; dTDP-glucose 4,6-hydro-lyase (dTDP-4-dehydro-6-deoxy-α-D-glucose-forming)
Systematic name: dTDP-α-D-glucose 4,6-hydro-lyase (dTDP-4-dehydro-6-deoxy-α-D-glucose-forming)
Comments: Requires bound NAD+.
References:
1.  Gilbert, J.M., Matsuhashi, M. and Strominger, J.L. Thymidine diphosphate 4-acetamido-4,6-dideoxyhexoses. II. Purification and properties of thymidine diphosphate D-glucose oxidoreductase. J. Biol. Chem. 240 (1965) 1305–1308. [PMID: 14284740]
2.  Melo, A., Elliott, H. and Glaser, L. The mechanism of 6-deoxyhexose synthesis. I. Intramolecular hydrogen transfer catalyzed by deoxythymidine diphosphate D-glucose oxidoreductase. J. Biol. Chem. 243 (1968) 1467–1474. [PMID: 4869560]
3.  Wang, S.-F. and Gabriel, O. Biological mechanisms involved in the formation of deoxy sugars. V. Isolation and crystallization of thymidine diphosphate-D-glucose oxidoreductase from Escherichia coli B. J. Biol. Chem. 244 (1969) 3430–3437. [PMID: 4307450]
4.  Hegeman, A.D., Gross, J.W. and Frey, P.A. Probing catalysis by Escherichia coli dTDP-glucose-4,6-dehydratase: identification and preliminary characterization of functional amino acid residues at the active site. Biochemistry 40 (2001) 6598–6610. [PMID: 11380254]
5.  Gross, J.W., Hegeman, A.D., Gerratana, B. and Frey, P.A. Dehydration is catalyzed by glutamate-136 and aspartic acid-135 active site residues in Escherichia coli dTDP-glucose 4,6-dehydratase. Biochemistry 40 (2001) 12497–12504. [PMID: 11601973]
[EC 4.2.1.46 created 1972]
 
 
EC 4.2.1.47     
Accepted name: GDP-mannose 4,6-dehydratase
Reaction: GDP-α-D-mannose = GDP-4-dehydro-α-D-rhamnose + H2O
Glossary: GDP-4-dehydro-α-D-rhamnose = GDP-4-dehydro-6-deoxy-α-D-mannose
Other name(s): guanosine 5′-diphosphate-D-mannose oxidoreductase; guanosine diphosphomannose oxidoreductase; guanosine diphosphomannose 4,6-dehydratase; GDP-D-mannose dehydratase; GDP-D-mannose 4,6-dehydratase; Gmd; GDP-mannose 4,6-hydro-lyase; GDP-mannose 4,6-hydro-lyase (GDP-4-dehydro-6-deoxy-D-mannose-forming)
Systematic name: GDP-α-D-mannose 4,6-hydro-lyase (GDP-4-dehydro-α-D-rhamnose-forming)
Comments: The bacterial enzyme requires bound NAD+. This enzyme forms the first step in the biosynthesis of GDP-α-D-rhamnose and GDP-β-L-fucose. In Aneurinibacillus thermoaerophilus L420-91T, this enzyme acts as a bifunctional enzyme, catalysing the above reaction as well as the reaction catalysed by EC 1.1.1.281, GDP-4-dehydro-6-deoxy-D-mannose reductase [5]. Belongs to the short-chain dehydrogenase/reductase enzyme family, having homologous structures and a conserved catalytic triad of Lys, Tyr and Ser/Thr residues [6].
References:
1.  Elbein, A.D. and Heath, E.C. The biosynthesis of cell wall lipopolysaccharide in Escherichia coli. II. Guanosine diphosphate 4-keto-6-deoxy-D-mannose, an intermediate in the biosynthesis of guanosine diphosphate colitose. J. Biol. Chem. 240 (1965) 1926–1931. [PMID: 14299611]
2.  Liao, T.-H. and Barber, G.A. Purification of guanosine 5′-diphosphate D-mannose oxidoreductase from Phaseolus vulgaris. Biochim. Biophys. Acta 276 (1972) 85–93. [PMID: 5047712]
3.  Melo, A., Elliott, H. and Glaser, L. The mechanism of 6-deoxyhexose synthesis. I. Intramolecular hydrogen transfer catalyzed by deoxythymidine diphosphate D-glucose oxidoreductase. J. Biol. Chem. 243 (1968) 1467–1474. [PMID: 4869560]
4.  Sullivan, F.X., Kumar, R., Kriz, R., Stahl, M., Xu, G.Y., Rouse, J., Chang, X.J., Boodhoo, A., Potvin, B. and Cumming, D.A. Molecular cloning of human GDP-mannose 4,6-dehydratase and reconstitution of GDP-fucose biosynthesis in vitro. J. Biol. Chem. 273 (1988) 8193–8202. [PMID: 9525924]
5.  Kneidinger, B., Graninger, M., Adam, G., Puchberger, M., Kosma, P., Zayni, S. and Messner, P. Identification of two GDP-6-deoxy-D-lyxo-4-hexulose reductases synthesizing GDP-D-rhamnose in Aneurinibacillus thermoaerophilus L420-91T. J. Biol. Chem. 276 (2001) 5577–5583. [PMID: 11096116]
6.  Mulichak, A.M., Bonin, C.P., Reiter, W.D. and Garavito, R.M. Structure of the MUR1 GDP-mannose 4,6-dehydratase from Arabidopsis thaliana: implications for ligand binding and specificity. Biochemistry 41 (2000) 15578–15589. [PMID: 12501186]
[EC 4.2.1.47 created 1972, modified 2004]
 
 
EC 4.2.1.48     
Accepted name: D-glutamate cyclase
Reaction: D-glutamate = 5-oxo-D-proline + H2O
Other name(s): D-glutamate hydro-lyase (cyclizing)
Systematic name: D-glutamate hydro-lyase (cyclizing; 5-oxo-D-proline-forming)
Comments: Also acts on various derivatives of D-glutamate.
References:
1.  Meister, A., Bukenberger, M.W. and Strassburger, M. The optically-specific enzymatic cyclization of D-glutamate. Biochem. Z. 338 (1963) 217–229. [PMID: 14087295]
[EC 4.2.1.48 created 1972]
 
 
EC 4.2.1.49     
Accepted name: urocanate hydratase
Reaction: 3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate = urocanate + H2O
Glossary: urocanate = (E)-3-(imidazol-4-yl)propenoate
Other name(s): urocanase; 3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate hydro-lyase
Systematic name: 3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate hydro-lyase (urocanate-forming)
Comments: Contains tightly bound NAD+.
References:
1.  Rétey, J. The urocanase story: a novel role of NAD+ as electrophile. Arch. Biochem. Biophys. 314 (1994) 1–16. [PMID: 7944380]
2.  Hassall, H. and Greenberg, D.M. Urocanase (beef liver). Methods Enzymol. 17B (1971) 84–88.
3.  Kaminskas, E., Kimhi, Y. and Magasanik, B. Urocanase and N-formimino-L-glutamate formiminohydrolase of Bacillus subtilis, two enzymes of the histidine degradation pathway. J. Biol. Chem. 245 (1970) 3536–3544. [PMID: 4990470]
4.  Swaine, D. The effect of substrate analogues on the activity of cat liver urocanase. Biochim. Biophys. Acta 178 (1969) 609–618. [PMID: 5784906]
[EC 4.2.1.49 created 1972, modified 2001]
 
 
EC 4.2.1.50     
Accepted name: pyrazolylalanine synthase
Reaction: L-serine + pyrazole = 3-(pyrazol-1-yl)-L-alanine + H2O
Other name(s): β-pyrazolylalaninase; β-(1-pyrazolyl)alanine synthase; L-serine hydro-lyase (adding pyrazole)
Systematic name: L-serine hydro-lyase [adding pyrazole; 3-(pyrazol-1-yl)-L-alanine-forming]
Comments: A pyridoxal-phosphate protein.
References:
1.  Dunnill, P.M. and Fowden, L. The biosynthesis of β-pyrazol-1-ylalanine. J. Exp. Bot. 14 (1963) 237–248.
[EC 4.2.1.50 created 1972]
 
 
EC 4.2.1.51     
Accepted name: prephenate dehydratase
Reaction: prephenate = phenylpyruvate + H2O + CO2
Other name(s): prephenate hydro-lyase (decarboxylating)
Systematic name: prephenate hydro-lyase (decarboxylating; phenylpyruvate-forming)
Comments: This enzyme in the enteric bacteria also possesses chorismate mutase (EC 5.4.99.5) activity, and converts chorismate into prephenate.
References:
1.  Cerutti, P. and Guroff, G. Enzymatic formation of phenylpyruvic acid in Pseudomonas sp. (ATCC 11299A) and its regulation. J. Biol. Chem. 240 (1965) 3034–3048. [PMID: 14342329]
2.  Cotton, R.G.H. and Gibson, F. The biosynthesis of phenylalanine and tyrosine; enzymes converting chorismic acid into prephenic acid and their relationships to prephenate dehydratase and prephenate dehydrogenase. Biochim. Biophys. Acta 100 (1965) 76–88. [PMID: 14323651]
3.  Schmidt, J.C. and Zalkin, H. Chorismate mutase-prephenate dehydratase. Partial purification and properties of the enzyme from Salmonella typhimurium. Biochemistry 8 (1969) 174–181. [PMID: 4887851]
[EC 4.2.1.51 created 1972]
 
 
EC 4.2.1.52      
Transferred entry: dihydrodipicolinate synthase. Now EC 4.3.3.7, 4-hydroxy-2,3,4,5-tetrahydrodipicolinate synthase.
[EC 4.2.1.52 created 1972, deleted 2012]
 
 
EC 4.2.1.53     
Accepted name: oleate hydratase
Reaction: (R)-10-hydroxystearate = oleate + H2O
Other name(s): (R)-10-hydroxystearate 10-hydro-lyase
Systematic name: (R)-10-hydroxystearate 10-hydro-lyase (oleate-forming)
Comments: Acts on a number of 10-hydroxy acids.
References:
1.  Davis, E.N., Wallen, L.L., Goodwin, J.C., Rohwedder, W.K. and Rhodes, R.A. Microbial hydration of cis-9-alkenoic acids. Lipids 4 (1969) 356–362. [PMID: 5823715]
2.  Gotouda, H., Takatori, T., Terazawa, K., Nagao, M. and Tarao, H. The mechanism of experimental adipocere formation: hydration and dehydrogenation in microbial synthesis of hydroxy and oxo fatty acids. Forensic Sci. Int. 37 (1988) 249–257. [PMID: 3410394]
3.  Niehaus, W.G., Jr., Kisic, A., Torkelson, A., Bednarczyk, D.J. and Schroepfer, G.J., Jr. , Stereospecific hydration of the Δ9 double bond of oleic acid. J. Biol. Chem. 245 (1970) 3790–3797. [PMID: 5492948]
[EC 4.2.1.53 created 1972]
 
 
EC 4.2.1.54     
Accepted name: lactoyl-CoA dehydratase
Reaction: (R)-lactoyl-CoA = acryloyl-CoA + H2O
Other name(s): lactoyl coenzyme A dehydratase; lactyl-coenzyme A dehydrase; lactyl CoA dehydratase; acrylyl coenzyme A hydratase; lactoyl-CoA hydro-lyase
Systematic name: (R)-lactoyl-CoA hydro-lyase (acryloyl-CoA-forming)
Comments: A bacterial enzyme that is involved in propanoate fermentation (also known as the acrylate pathway).
References:
1.  Baldwin, R.L., Wood, W.A. and Emery, R.S. Lactate metabolism by Peptostreptococcus elsdenii: evidence for lactyl coenzyme a dehydrase. Biochim. Biophys. Acta 97 (1965) 202–213. [PMID: 14292829]
2.  Schweiger, G. and Buckel, W. On the dehydration of (R)-lactate in the fermentation of alanine to propionate by Clostridium propionicum. FEBS Lett. 171 (1984) 79–84. [PMID: 6586495]
3.  Kuchta, R.D. and Abeles, R.H. Lactate reduction in Clostridium propionicum. Purification and properties of lactyl-CoA dehydratase. J. Biol. Chem. 260 (1985) 13181–13189. [PMID: 4055736]
4.  Kuchta, R.D., Hanson, G.R., Holmquist, B. and Abeles, R.H. Fe-S centers in lactyl-CoA dehydratase. Biochemistry 25 (1986) 7301–7307. [PMID: 3026450]
5.  Hofmeister, A.E. and Buckel, W. (R)-Lactyl-CoA dehydratase from Clostridium propionicum. Stereochemistry of the dehydration of (R)-2-hydroxybutyryl-CoA to crotonyl-CoA. Eur. J. Biochem. 206 (1992) 547–552. [PMID: 1597194]
[EC 4.2.1.54 created 1972, modified 2012]
 
 
EC 4.2.1.55     
Accepted name: 3-hydroxybutyryl-CoA dehydratase
Reaction: (3R)-3-hydroxybutanoyl-CoA = crotonoyl-CoA + H2O
Other name(s): D-3-hydroxybutyryl coenzyme A dehydratase; D-3-hydroxybutyryl-CoA dehydratase; enoyl coenzyme A hydrase (D); (3R)-3-hydroxybutanoyl-CoA hydro-lyase
Systematic name: (3R)-3-hydroxybutanoyl-CoA hydro-lyase (crotonoyl-CoA-forming)
Comments: Also acts on crotonoyl thioesters of pantetheine and acyl-carrier protein.
References:
1.  Moskowitz, G.J. and Merrick, J.M. Metabolism of poly-β-hydroxybutyrate. II. Enzymatic synthesis of D-(-)-β-hydroxybutyryl coenzyme A by an enoyl hydrase from Rhodospirillum rubrum. Biochemistry 8 (1969) 2748–2755. [PMID: 5808333]
[EC 4.2.1.55 created 1972]
 
 
EC 4.2.1.56     
Accepted name: itaconyl-CoA hydratase
Reaction: citramalyl-CoA = itaconyl-CoA + H2O
Other name(s): itaconyl coenzyme A hydratase; citramalyl-CoA hydro-lyase
Systematic name: citramalyl-CoA hydro-lyase (itaconyl-CoA-forming)
References:
1.  Cooper, R.A. and Kornberg, H.L. The utilization of itaconate by Pseudomonas sp. Biochem. J. 91 (1964) 82–91. [PMID: 4284209]
[EC 4.2.1.56 created 1972]
 
 
EC 4.2.1.57     
Accepted name: isohexenylglutaconyl-CoA hydratase
Reaction: 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA = 3-(4-methylpent-3-en-1-yl)pent-2-enedioyl-CoA + H2O
Other name(s): 3-hydroxy-3-isohexenylglutaryl-CoA-hydrolase; isohexenylglutaconyl coenzyme A hydratase; β-isohexenylglutaconyl-CoA-hydratase; 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA hydro-lyase
Systematic name: 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA hydro-lyase [3-(4-methylpent-3-en-1-yl)pent-2-enedioyl-CoA-forming]
Comments: Also acts on dimethylacryloyl-CoA and farnesoyl-CoA.
References:
1.  Seubert, W. and Fass, E. Untersuchungen über den bakterielle Abbau von Isoprenoiden. IV. Reinigung und Eigenschaftender β-Isohexenylglutaconyl-CoA-hydratase und β-Hydroxy-β-isohexenylglutaryl-CoA-lyase. Biochem. Z. 341 (1964) 23–34. [PMID: 14339651]
[EC 4.2.1.57 created 1972]
 
 
EC 4.2.1.58      
Deleted entry: crotonoyl-[acyl-carrier-protein] hydratase. The reaction described is covered by EC 4.2.1.59.
[EC 4.2.1.58 created 1972, deleted 2012]
 
 
EC 4.2.1.59     
Accepted name: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
Reaction: a (3R)-3-hydroxyacyl-[acyl-carrier protein] = a trans-2-enoyl-[acyl-carrier protein] + H2O
Other name(s): fabZ (gene name); fabA (gene name); D-3-hydroxyoctanoyl-[acyl carrier protein] dehydratase; D-3-hydroxyoctanoyl-acyl carrier protein dehydratase; β-hydroxyoctanoyl-acyl carrier protein dehydrase; β-hydroxyoctanoyl thioester dehydratase; β-hydroxyoctanoyl-ACP-dehydrase; (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] hydro-lyase; (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] hydro-lyase (oct-2-enoyl-[acyl-carrier protein]-forming); 3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase
Systematic name: (3R)-3-hydroxyacyl-[acyl-carrier protein] hydro-lyase (trans-2-enoyl-[acyl-carrier protein]-forming)
Comments: This enzyme is responsible for the dehydration step of the dissociated (type II) fatty-acid biosynthesis system that occurs in plants and bacteria. The enzyme uses fatty acyl thioesters of ACP in vivo. Different forms of the enzyme may have preferences for substrates with different chain length. For example, the activity of FabZ, the ubiquitous enzyme in bacteria, decreases with increasing chain length. Gram-negative bacteria that produce unsaturated fatty acids, such as Escherichia coli, have another form (FabA) that prefers intermediate chain length, and also catalyses EC 5.3.3.14, trans-2-decenoyl-[acyl-carrier protein] isomerase. Despite the differences both forms can catalyse all steps leading to the synthesis of palmitate (C16:0). FabZ, but not FabA, can also accept unsaturated substrates [4].
References:
1.  Mizugaki, M., Swindell, A.C. and Wkil, S.J. Intermediate- and long-chain β-hydroxyacyl-ACP dehydrases from E. coli fatty acid synthetase. Biochem. Biophys. Res. Commun. 33 (1968) 520–527. [PMID: 4881058]
2.  Sharma, A., Henderson, B.S., Schwab, J.M. and Smith, J.L. Crystallization and preliminary X-ray analysis of β-hydroxydecanoyl thiol ester dehydrase from Escherichia coli. J. Biol. Chem. 265 (1990) 5110–5112. [PMID: 2180957]
3.  Mohan, S., Kelly, T.M., Eveland, S.S., Raetz, C.R. and Anderson, M.S. An Escherichia coli gene (FabZ) encoding (3R)-hydroxymyristoyl acyl carrier protein dehydrase. Relation to fabA and suppression of mutations in lipid A biosynthesis. J. Biol. Chem. 269 (1994) 32896–32903. [PMID: 7806516]
4.  Heath, R.J. and Rock, C.O. Roles of the FabA and FabZ β-hydroxyacyl-acyl carrier protein dehydratases in Escherichia coli fatty acid biosynthesis. J. Biol. Chem. 271 (1996) 27795–27801. [PMID: 8910376]
[EC 4.2.1.59 created 1972, modified 2012]
 
 
EC 4.2.1.60      
Deleted entry: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase. The reaction described is covered by EC 4.2.1.59.
[EC 4.2.1.60 created 1972, modified 2006, deleted 2012]
 
 
EC 4.2.1.61      
Deleted entry: 3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase. The reaction described is covered by EC 4.2.1.59.
[EC 4.2.1.61 created 1972, deleted 2012]
 
 
EC 4.2.1.62     
Accepted name: 5α-hydroxysteroid dehydratase
Reaction: 5α-ergosta-7,22-diene-3β,5-diol = ergosterol + H2O
Other name(s): 5α-ergosta-7,22-diene-3β,5-diol 5,6-hydro-lyase
Systematic name: 5α-ergosta-7,22-diene-3β,5-diol 5,6-hydro-lyase (ergosterol-forming)
References:
1.  Topham, R.W. and Gaylor, J.L. Isolation and purification of a 5α-hydroxysterol dehydrase of yeast. J. Biol. Chem. 245 (1970) 2319–2327. [PMID: 5442273]
[EC 4.2.1.62 created 1972]
 
 
EC 4.2.1.63      
Transferred entry: epoxide hydratase. Now known to comprise two enzymes, microsomal epoxide hydrolase (EC 3.3.2.9) and soluble epoxide hydrolase (EC 3.3.2.10)
[EC 4.2.1.63 created 1972, deleted 1978]
 
 
EC 4.2.1.64      
Transferred entry: arene-oxide hydratase. Now known to comprise two enzymes, microsomal epoxide hydrolase (EC 3.3.2.9) and soluble epoxide hydrolase (EC 3.3.2.10)
[EC 4.2.1.64 created 1972, deleted 1978]
 
 
EC 4.2.1.65     
Accepted name: 3-cyanoalanine hydratase
Reaction: L-asparagine = 3-cyanoalanine + H2O
Other name(s): β-cyanoalanine hydrolase; β-cyanoalanine hydratase; β-CNAla hydrolase; β-CNA nitrilase; L-asparagine hydro-lyase
Systematic name: L-asparagine hydro-lyase (3-cyanoalanine-forming)
References:
1.  Castric, P.A., Farnden, K.J.F. and Conn, E.E. Cyanide metabolism in higher plants. V. The formation of asparagine from β-cyanoalanine. Arch. Biochem. Biophys. 152 (1972) 62–69. [PMID: 4627358]
[EC 4.2.1.65 created 1976]
 
 
EC 4.2.1.66     
Accepted name: cyanide hydratase
Reaction: formamide = cyanide + H2O
Other name(s): formamide dehydratase; formamide hydro-lyase
Systematic name: formamide hydro-lyase (cyanide-forming)
References:
1.  Fry, W.E. and Millar, R.L. Cyanide degradion by an enzyme from Stemphylium loti. Arch. Biochem. Biophys. 151 (1972) 468–474. [PMID: 5065258]
[EC 4.2.1.66 created 1976]
 
 
EC 4.2.1.67     
Accepted name: D-fuconate dehydratase
Reaction: D-fuconate = 2-dehydro-3-deoxy-D-fuconate + H2O
Other name(s): D-fuconate hydro-lyase
Systematic name: D-fuconate hydro-lyase (2-dehydro-3-deoxy-D-fuconate-forming)
Comments: Also acts on L-arabinonate.
References:
1.  Dahms, A.S. and Anderson, R.L. D-Fucose metabolism in a pseudomonad. 3. Conversion of D-fuconate to 2-keto-3-deoxy-D-fuconate by a dehydratase. J. Biol. Chem. 247 (1972) 2233–2237. [PMID: 4335868]
[EC 4.2.1.67 created 1976]
 
 
EC 4.2.1.68     
Accepted name: L-fuconate dehydratase
Reaction: L-fuconate = 2-dehydro-3-deoxy-L-fuconate + H2O
Other name(s): L-fuconate hydro-lyase
Systematic name: L-fuconate hydro-lyase (2-dehydro-3-deoxy-L-fuconate-forming)
Comments: Also acts, slowly, on D-arabinonate.
References:
1.  Yuen, R. and Schachter, H. L-Fucose metabolism in mammals. I. Pork liver L-fuconate hydro-lyase. Can. J. Biochem. 50 (1972) 798–806. [PMID: 5050937]
[EC 4.2.1.68 created 1976]
 
 
EC 4.2.1.69     
Accepted name: cyanamide hydratase
Reaction: urea = cyanamide + H2O
Other name(s): urea hydro-lyase
Systematic name: urea hydro-lyase (cyanamide-forming)
References:
1.  Stransky, H. and Amberger, A. Isolation and properties of a cyanamide hydratase (EC 4.2.1) from Myrothecium verrucaria. Z. Pflanzenphysiol. 70 (1973) 74–87.
[EC 4.2.1.69 created 1976]
 
 
EC 4.2.1.70     
Accepted name: pseudouridylate synthase
Reaction: uracil + D-ribose 5-phosphate = pseudouridine 5′-phosphate + H2O
Other name(s): pseudouridylic acid synthetase; pseudouridine monophosphate synthetase; 5-ribosyluracil 5-phosphate synthetase; pseudouridylate synthetase; upsilonUMP synthetase; uracil hydro-lyase (adding D-ribose 5-phosphate); YeiN; pseudouridine-5′-phosphate glycosidase
Systematic name: uracil hydro-lyase (adding D-ribose 5-phosphate; pseudouridine-5′-phosphate-forming)
Comments: The reaction it readily reversible. While the enzymes from Tetrahymena pyriformis and Agrobacterium tumefaciens produce pseudouridine 5′-phosphate the enzyme from Escherichia coli functions as a pseudouridine-5′-phosphate glycosidase in vivo [5].
References:
1.  Heinrikson, R.L. and Goldwasser, E. Studies on the biosynthesis of 5-ribosyluracil 5′-monophosphate in Tetrahymena pyriformis. J. Biol. Chem. 239 (1964) 1177–1187. [PMID: 14165924]
2.  Matsushita, T. and Davis, F.F. Studies on pseudouridylic acid synthetase from various sources. Biochim. Biophys. Acta 238 (1971) 165–173. [PMID: 4936431]
3.  Rensen, J.F., Matsushita, T., Chirikjian, J.G. and Davis, F.F. Enzymatic synthesis of deoxypseudouridylic acid and a study of certain of its properties. Biochim. Biophys. Acta 281 (1972) 481–487. [PMID: 4569284]
4.  Suzuki, T. and Hochater, R.M. On the biosynthesis of pseudouridine and of pseudouridylic acid in Agrobacterium tumefaciens. Can. J. Biochem. 44 (1966) 259–272. [PMID: 5942965]
5.  Preumont, A., Snoussi, K., Stroobant, V., Collet, J.F. and Van Schaftingen, E. Molecular identification of pseudouridine-metabolizing enzymes. J. Biol. Chem. 283 (2008) 25238–25246. [PMID: 18591240]
[EC 4.2.1.70 created 1978]
 
 
EC 4.2.1.71      
Deleted entry:  acetylenecarboxylate hydratase. This enzyme is identical to EC 4.2.1.27, acetylenecarboxylate hydratase
[EC 4.2.1.71 created 1978, modified 1989, modified 2000, deleted 2004]
 
 
EC 4.2.1.72      
Transferred entry: acetylenedicarboxylate hydratase. Now EC 4.1.1.78, acetylenedicarboxylate decarboxylase
[EC 4.2.1.72 created 1978, deleted 2000]
 
 
EC 4.2.1.73     
Accepted name: protoaphin-aglucone dehydratase (cyclizing)
Reaction: protoaphin aglucone = xanthoaphin + H2O
Other name(s): protoaphin dehydratase; protoaphin dehydratase (cyclizing); protoaphin-aglucone hydro-lyase (cyclizing)
Systematic name: protoaphin-aglucone hydro-lyase (cyclizing; xanthoaphin-forming)
Comments: The product is converted non-enzymically to erythroaphin, an aphid pigment.
References:
1.  Cameron, D.W., Sawyer, W.H. and Trikojus, V.M. Colouring matters of the Aphidoidea. XLII. Purification and properties of the cyclising enzyme [Protoaphin dehydratase (cyclising)] concerned with pigment transformation in the wooly aphid Eriosoma lanigerum Hausmann (Hemiptera: Insecta). Aust. J. Biol. Sci. 30 (1977) 173–181.
[EC 4.2.1.73 created 1978]
 
 
EC 4.2.1.74     
Accepted name: long-chain-enoyl-CoA hydratase
Reaction: a long-chain (3S)-3-hydroxyacyl-CoA = a long-chain trans-2-enoyl-CoA + H2O
Glossary: a long-chain acyl-CoA = an acyl-CoA thioester where the acyl chain contains 13 to 22 carbon atoms.
Other name(s): long-chain enoyl coenzyme A hydratase
Systematic name: long-chain-(3S)-3-hydroxyacyl-CoA hydro-lyase
Comments: Acts in the reverse direction. The best substrate is oct-3-enoyl-CoA. Unlike EC 4.2.1.17 enoyl-CoA hydratase, it does not act on crotonoyl-CoA.
References:
1.  Fong, J.C. and Schulz, H. Purification and properties of pig heart crotonase and the presence of short chain and long chain enoyl coenzyme A hydratases in pig and guinea pig tissues. J. Biol. Chem. 252 (1977) 542–547. [PMID: 833142]
2.  Schulz, H. Long chain enoyl coenzyme A hydratase from pig heart. J. Biol. Chem. 249 (1974) 2704–2709. [PMID: 4828315]
[EC 4.2.1.74 created 1981]
 
 
EC 4.2.1.75     
Accepted name: uroporphyrinogen-III synthase
Reaction: hydroxymethylbilane = uroporphyrinogen III + H2O
Other name(s): porphobilinogenase; uroporphyrinogen isomerase; uroporphyrinogen III cosynthase; URO-synthase; hydroxymethylbilane hydro-lyase (cyclizing)
Systematic name: hydroxymethylbilane hydro-lyase (cyclizing; uroporphyrinogen-III-forming)
Comments: In the presence of EC 2.5.1.61, hydroxymethylbilane synthase, the enzyme forms uroporphyrinogen III from porphobilinogen.
References:
1.  Battersby, A.R., Fookes, C.J.R., Matcham, G.W.J. and McDonald, E. Biosynthesis of the pigments of life: formation of the macrocycle. Nature 285 (1980) 17–21. [PMID: 6769048]
2.  Tsai, S.-F., Bishop, D.F. and Desnick, R.J. Purification and properties of uroporphyrinogen III synthase from human erythrocytes. J. Biol. Chem. 262 (1987) 1268–1273. [PMID: 3805019]
[EC 4.2.1.75 created 1982]
 
 
EC 4.2.1.76     
Accepted name: UDP-glucose 4,6-dehydratase
Reaction: UDP-α-D-glucose = UDP-4-dehydro-6-deoxy-α-D-glucose + H2O
Other name(s): UDP-D-glucose-4,6-hydrolyase; UDP-D-glucose oxidoreductase; UDP-glucose 4,6-hydro-lyase
Systematic name: UDP-α-D-glucose 4,6-hydro-lyase (UDP-4-dehydro-6-deoxy-α-D-glucose-forming)
References:
1.  Kamsteeg, J., van Brederode, J. and van Nigtevecht, G. The formation of UDP-L-rhamnose from UDP-D-glucose by an enzyme preparation of red campion (Silene dioica (L) Clairv) leaves. FEBS Lett. 91 (1978) 281–284. [PMID: 680134]
[EC 4.2.1.76 created 1984]
 
 
EC 4.2.1.77     
Accepted name: trans-L-3-hydroxyproline dehydratase
Reaction: trans-3-hydroxy-L-proline = 1-pyrroline 2-carboxylate + H2O
Other name(s): trans-L-3-hydroxyproline hydro-lyase
Systematic name: trans-3-hydroxy-L-proline hydro-lyase (1-pyrroline-2-carboxylate-forming)
Comments: Highly specific.
References:
1.  Ramaswamy, S.G. Conversion of 3-hydroxyproline to proline in the rat requires reduced pyridine-nucleotides. Fed. Proc. 42 (1983) 2232.
2.  Visser, W.F., Verhoeven-Duif, N.M. and de Koning, T.J. Identification of a human trans-3-hydroxy-L-proline dehydratase, the first characterized member of a novel family of proline racemase-like enzymes. J. Biol. Chem. 287 (2012) 21654–21662. [PMID: 22528483]
[EC 4.2.1.77 created 1984]
 
 
EC 4.2.1.78     
Accepted name: (S)-norcoclaurine synthase
Reaction: 4-hydroxyphenylacetaldehyde + dopamine = (S)-norcoclaurine + H2O
Glossary: dopamine = 4-(2-aminoethyl)benzene-1,2-diol
Other name(s): (S)-norlaudanosoline synthase; 4-hydroxyphenylacetaldehyde hydro-lyase (adding dopamine)
Systematic name: 4-hydroxyphenylacetaldehyde hydro-lyase [adding dopamine; (S)-norcoclaurine-forming]
Comments: The reaction makes a six-membered ring by forming a bond between C-6 of the 3,4-dihydroxyphenyl group of the dopamine and C-1 of the aldehyde in the imine formed between the substrates. The product is the precursor of the benzylisoquinoline alkaloids in plants. The enzyme, formerly known as (S)-norlaudanosoline synthase, will also catalyse the reaction of 4-(2-aminoethyl)benzene-1,2-diol + (3,4-dihydroxyphenyl)acetaldehyde to form (S)-norlaudanosoline, but this alkaloid has not been found to occur in plants.
References:
1.  Stadler, R., Zenk, M.H. A revision of the generally accepted pathway for the biosynthesis of the benzyltetrahydroisoquinoline reticuline. Liebigs Ann. Chem. (1990) 555–562.
2.  Stadler, R., Kutchan, T.M., Zenk, M.H. (S)-Norcoclaurine is the central intermediate in benzylisoquinoline alkaloid biosynthesis. Phytochemistry 28 (1989) 1083–1086.
3.  Samanani, N. and Facchini, P.J. Purification and characterization of norcoclaurine synthase. The first committed enzyme in benzylisoquinoline alkaloid biosynthesis in plants. J. Biol. Chem. 277 (2002) 33878–33883. [PMID: 12107162]
[EC 4.2.1.78 created 1984, modified 1999]
 
 
EC 4.2.1.79     
Accepted name: 2-methylcitrate dehydratase
Reaction: (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate = (Z)-but-2-ene-1,2,3-tricarboxylate + H2O
Glossary: (2S,3S)-2-methylcitrate = (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate
cis-2-methylaconitate = (Z)-but-2-ene-1,2,3-tricarboxylate
Other name(s): 2-methylcitrate hydro-lyase; PrpD; 2-hydroxybutane-1,2,3-tricarboxylate hydro-lyase
Systematic name: (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate hydro-lyase [(Z)-but-2-ene-1,2,3-tricarboxylate-forming]
Comments: The enzyme is specific for (2S,3S)-methylcitrate, showing no activity with (2R,3S)-methylcitrate [2]. The enzyme can also use cis-aconitate as a substrate but more slowly [2]. Both this enzyme and EC 4.2.1.3, aconitate hydratase, are required to complete the isomerization of (2S,3S)-methylcitrate to (2R,3S)-2-methylisocitrate [2].
References:
1.  Aoki, H. and Tabuchi, T. Purification and properties of 2-methylcitrate dehydratase from Yarrowia lipolytica. Agric. Biol. Chem. 45 (1981) 2831–2837.
2.  Brock, M., Maerker, C., Schütz, A., Völker, U. and Buckel, W. Oxidation of propionate to pyruvate in Escherichia coli. Involvement of methylcitrate dehydratase and aconitase. Eur. J. Biochem. 269 (2002) 6184–6194. [PMID: 12473114]
[EC 4.2.1.79 created 1984]
 
 
EC 4.2.1.80     
Accepted name: 2-oxopent-4-enoate hydratase
Reaction: (S)-4-hydroxy-2-oxopentanoate = (2Z)-2-hydroxypenta-2,4-dienoate + H2O
Other name(s): 2-keto-4-pentenoate hydratase; OEH; 2-keto-4-pentenoate (vinylpyruvate)hydratase; 4-hydroxy-2-oxopentanoate hydro-lyase; 4-hydroxy-2-oxopentanoate hydro-lyase (2-oxopent-4-enoate-forming); mhpD (gene name); ahdF (gene name); todG (gene name); cmtF (gene name); xylJ (gene name); cnbE (gene name)
Systematic name: (S)-4-hydroxy-2-oxopentanoate hydro-lyase ((2Z)-2-hydroxypenta-2,4-dienoate-forming)
Comments: The enzyme is involved in the catechol meta-cleavage pathway, a major mechanism for degradation of aromatic compounds. Also acts, more slowly, on cis-2-oxohex-4-enoate, but not on the trans-isomer. The enzyme was named when it was thought that the substrate is 2-oxopent-4-enoate. However, it was later found that the actual substrate is its tautomer (2Z)-2-hydroxypenta-2,4-dienoate. In some organisms the enzyme forms a complex with EC 4.1.1.77, 2-oxo-3-hexenedioate decarboxylase (previously named 4-oxalocrotonate decarboxylase).
References:
1.  Kunz, D.A., Ribbons, D.W. and Chapman, P.J. Metabolism of allylglycine and cis-crotylglycine by Pseudomonas putida (arvilla) mt-2 harboring a TOL plasmid. J. Bacteriol. 148 (1981) 72–82. [PMID: 7287632]
2.  Harayama, S., Rekik, M., Ngai, K.L. and Ornston, L.N. Physically associated enzymes produce and metabolize 2-hydroxy-2,4-dienoate, a chemically unstable intermediate formed in catechol metabolism via meta cleavage in Pseudomonas putida. J. Bacteriol. 171 (1989) 6251–6258. [PMID: 2681159]
3.  Pollard, J.R. and Bugg, T.D. Purification, characterisation and reaction mechanism of monofunctional 2-hydroxypentadienoic acid hydratase from Escherichia coli. Eur. J. Biochem. 251 (1998) 98–106. [PMID: 9492273]
[EC 4.2.1.80 created 1984]
 
 
EC 4.2.1.81     
Accepted name: D(-)-tartrate dehydratase
Reaction: (S,S)-tartrate = oxaloacetate + H2O
Other name(s): D-tartrate dehydratase; (S,S)-tartrate hydro-lyase
Systematic name: (S,S)-tartrate hydro-lyase (oxaloacetate-forming)
Comments: Requires Fe2+ or Mn2+. cf. EC 4.2.1.32 L(+)-tartrate dehydratase.
References:
1.  Rode, H. and Giffhorn, F. D-(-)-Tartrate dehydratase of Rhodopseudomonas sphaeroides: purification, characterization, and application to enzymatic determination of D-(-)-tartrate. J. Bacteriol. 150 (1982) 1061–1068. [PMID: 6978882]
2.  Rode, H. and Giffhorn, F. Ferrous- or cobalt ion-dependent D-(-)-tartrate dehydratase of pseudomonads: purification and properties. J. Bacteriol. 151 (1982) 1602–1604. [PMID: 7107563]
[EC 4.2.1.81 created 1986]
 
 
EC 4.2.1.82     
Accepted name: xylonate dehydratase
Reaction: D-xylonate = 2-dehydro-3-deoxy-D-arabinonate + H2O
Glossary: 2-dehydro-3-deoxy-D-arabinonate = 2-dehydro-3-deoxy-D-xylonate = 3-deoxy-L-glycero-pent-2-ulonate
Other name(s): D-xylo-aldonate dehydratase; D-xylonate dehydratase; D-xylonate hydro-lyase
Systematic name: D-xylonate hydro-lyase (2-dehydro-3-deoxy-D-arabinonate-forming)
References:
1.  Dahms, A.S. and Donald, A. D-xylo-Aldonate dehydratase. Methods Enzymol. 90 (1982) 302–305. [PMID: 7154961]
2.  Donald, A., Sibley, D., Lyons, D.E. and Dahms, A.S. D-Galactonate dehydrase. Purification and properties. J. Biol. Chem. 254 (1979) 2132–2137. [PMID: 422572]
[EC 4.2.1.82 created 1986]
 
 
EC 4.2.1.83     
Accepted name: 4-oxalomesaconate hydratase
Reaction: 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate = (1E,3E)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate + H2O
Other name(s): 4-oxalmesaconate hydratase; 4-carboxy-2-oxohexenedioate hydratase; 4-carboxy-2-oxobutane-1,2,4-tricarboxylate 2,3-hydro-lyase; oxalmesaconate hydratase; γ-oxalmesaconate hydratase; 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate 2,3-hydro-lyase; LigJ; GalB
Systematic name: (1E,3E)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate 1,2-hydro-lyase (2-hydroxy-4-oxobutane-1,2,4-tricarboxylate-forming)
Comments: This enzyme participates in the degradation of 3,4-dihydroxybenzoate (via the meta-cleavage pathway), syringate and 3,4,5-trihydroxybenzoate, catalysing the reaction in the opposite direction [1-3]. It accepts the enol-form of 4-oxalomesaconate, 2-hydroxy-4-carboxy-hexa-2,4-dienedioate [4].
References:
1.  Maruyama, K. Enzymes responsible for degradation of 4-oxalmesaconic acid in Pseudomonas ochraceae. J. Biochem. 93 (1983) 567–574. [PMID: 6841354]
2.  Maruyama, K. Purification and properties of γ-oxalomesaconate hydratase from Pseudomonas ochraceae grown with phthalate. Biochem. Biophys. Res. Commun. 128 (1985) 271–277. [PMID: 3985968]
3.  Hara, H., Masai, E., Katayama, Y. and Fukuda, M. The 4-oxalomesaconate hydratase gene, involved in the protocatechuate 4,5-cleavage pathway, is essential to vanillate and syringate degradation in Sphingomonas paucimobilis SYK-6. J. Bacteriol. 182 (2000) 6950–6957. [PMID: 11092855]
4.  Nogales, J., Canales, A., Jiménez-Barbero, J., Serra B., Pingarrón, J. M., García, J. L. and Díaz, E. Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida. Mol. Microbiol. 79 (2011) 359–374. [PMID: 21219457]
[EC 4.2.1.83 created 1986, modified 2011]
 
 
EC 4.2.1.84     
Accepted name: nitrile hydratase
Reaction: an aliphatic amide = a nitrile + H2O
Other name(s): nitrilase (ambiguous); 3-cyanopyridine hydratase; NHase; L-NHase; H-NHase; acrylonitrile hydratase; aliphatic nitrile hydratase; nitrile hydro-lyase
Systematic name: aliphatic-amide hydro-lyase (nitrile-forming)
Comments: Acts on short-chain aliphatic nitriles, converting them into the corresponding amides. Does not act on these amides or on aromatic nitriles. cf. EC 3.5.5.1 nitrilase.
References:
1.  Asano, Y., Fujishiro, K., Tani, Y. and Yamada, H. Microbial degradation of nitrile compounds. 5. Aliphatic nitrile hydratase from Arthrobacter sp J-1. Purification and characterization. Agric. Biol. Chem. 46 (1982) 1165–1174.
[EC 4.2.1.84 created 1989]
 
 
EC 4.2.1.85     
Accepted name: dimethylmaleate hydratase
Reaction: (2R,3S)-2,3-dimethylmalate = dimethylmaleate + H2O
Other name(s): (2R,3S)-2,3-dimethylmalate hydro-lyase
Systematic name: (2R,3S)-2,3-dimethylmalate hydro-lyase (dimethylmaleate-forming)
Comments: Requires Fe2+. Inhibited by oxygen.
References:
1.  Kollmann-Koch, A. and Eggerer, H. Nicotinic acid metabolism. Dimethylmaleate hydratase. Hoppe-Seyler's Z. Physiol. Chem. 365 (1984) 847–857. [PMID: 6489933]
[EC 4.2.1.85 created 1989]
 
 
EC 4.2.1.86      
Deleted entry:  16-dehydroprogesterone hydratase (reaction is identical to that of EC 4.2.1.98, 16α-hydroxyprogesterone dehydratase)
[EC 4.2.1.86 created 1989, deleted 2004]
 
 
EC 4.2.1.87     
Accepted name: octopamine dehydratase
Reaction: 1-(4-hydroxyphenyl)-2-aminoethanol = (4-hydroxyphenyl)acetaldehyde + NH3
Glossary: octopamine = 1-(4-hydroxyphenyl)-2-aminoethanol
Other name(s): octopamine hydrolyase; octopamine hydro-lyase (deaminating)
Systematic name: 1-(4-hydroxyphenyl)-2-aminoethanol hydro-lyase [deaminating; (4-hydroxyphenyl)acetaldehyde-forming]
Comments: The enzyme-catalysed reaction is believed to be dehydration to an enamine, which is spontaneously hydrolysed to an aldehyde and ammonia.
References:
1.  Cuskey, S.M., Peccoraro, V. and Olsen, R.H. Initial catabolism of aromatic biogenic amines by Pseudomonas aeruginosa PAO: pathway description, mapping of mutations, and cloning of essential genes. J. Bacteriol. 169 (1987) 2398–2404. [PMID: 3034855]
[EC 4.2.1.87 created 1989]
 
 
EC 4.2.1.88     
Accepted name: synephrine dehydratase
Reaction: (R)-synephrine = (4-hydroxyphenyl)acetaldehyde + methylamine
Glossary: (R)-synephrine = D-(-)-synephrine = 4-[(1R)-1-hydroxy-2-(methylamino)ethyl]phenol
Other name(s): syringinase
Systematic name: (R)-synephrine hydro-lyase (methylamine-forming)
Comments: Removal of H2O from (R)-synephrine produces a 2,3-enamine, which hydrolyses to the products shown in the reaction above. The enzyme from Arthrobacter synephrinum is highly specific [1].
References:
1.  Veeraswamy, M., Devi, N.A., Krishnan Kutty, R. and Subba Rao, P.V. Conversion of (±) synephrine into p-hydroxyphenylacetaldehyde by Arthrobacter synephrinum. A novel enzymic reaction. Biochem. J. 159 (1976) 807–809. [PMID: 1008837]
2.  Manne, V., Kutty, K.R. and Pillarisetti, S.R. Purification and properties of synephrinase from Arthrobacter synephrinum. Arch. Biochem. Biophys. 248 (1986) 324–334. [PMID: 3729420]
[EC 4.2.1.88 created 1989, modified 2012]
 
 
EC 4.2.1.89      
Deleted entry: carnitine dehydratase. The activity has now been shown to be due to EC 2.8.3.21, L-carnitine CoA-transferase and EC 4.2.1.149, crotonobetainyl-CoA hydratase.
[EC 4.2.1.89 created 1989, deleted 2014]
 
 
EC 4.2.1.90     
Accepted name: L-rhamnonate dehydratase
Reaction: L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H2O
Other name(s): L-rhamnonate hydro-lyase
Systematic name: L-rhamnonate hydro-lyase (2-dehydro-3-deoxy-L-rhamnonate-forming)
References:
1.  Rigo, L.U., Maréchal, L.R., Vieira, M.M. and Veiga, L.A. Oxidative pathway for L-rhamnose degradation in Pallularia pullulans. Can. J. Microbiol. 31 (1985) 817–822.
[EC 4.2.1.90 created 1989]
 
 
EC 4.2.1.91     
Accepted name: arogenate dehydratase
Reaction: L-arogenate = L-phenylalanine + H2O + CO2
Other name(s): carboxycyclohexadienyl dehydratase; L-arogenate hydro-lyase (decarboxylating)
Systematic name: L-arogenate hydro-lyase (decarboxylating; L-phenylalanine-forming)
Comments: Also acts on prephenate and D-prephenyllactate. cf. EC 4.2.1.51, prephenate dehydratase.
References:
1.  Fischer, R. and Jensen, R. Arogenate dehydratase. Methods Enzymol. 142 (1987) 495–502. [PMID: 3600377]
2.  Zamir, L.O., Tiberio, R., Devor, K.A., Sauriol, F., Ahmad, S. and Jensen, R.A. Structure of D-prephenyllactate. A carboxycyclohexadienyl metabolite from Neurospora crassa. J. Biol. Chem. 263 (1988) 17284–17290. [PMID: 2972718]
3.  Siehl, D.L. and Conn, E.E. Kinetic and regulatory properties of arogenate dehydratase in seedlings of Sorghum bicolor (L.) Moench. Arch. Biochem. Biophys. 260 (1988) 822–829. [PMID: 3124763]
[EC 4.2.1.91 created 1992, modified 2005]
 
 
EC 4.2.1.92     
Accepted name: hydroperoxide dehydratase
Reaction: (9Z,11E,15Z)-(13S)-hydroperoxyoctadeca-9,11,15-trienoate = (9Z,15Z)-(13S)-12,13-epoxyoctadeca-9,11,15-trienoate + H2O
Glossary: 13-hydroperoxylinolenoate = (9Z,11E,15Z)-(13S)-hydroperoxyoctadeca-9,11,15-trienoate
Other name(s): hydroperoxide isomerase; linoleate hydroperoxide isomerase; linoleic acid hydroperoxide isomerase; HPI; (9Z,11E,14Z)-(13S)-hydroperoxyoctadeca-9,11,14-trienoate 12,13-hydro-lyase; (9Z,11E,14Z)-(13S)-hydroperoxyoctadeca-9,11,14-trienoate 12,13-hydro-lyase [(9Z)-(13S)-12,13-epoxyoctadeca-9,11-dienoate-forming]; allene oxide synthase; AOS
Systematic name: (9Z,11E,15Z)-(13S)-hydroperoxyoctadeca-9,11,15-trienoate 12,13-hydro-lyase [(9Z,15Z)-(13S)-12,13-epoxyoctadeca-9,11,15-trienoate-forming]
Comments: Acts on a number of unsaturated fatty-acid hydroperoxides, forming the corresponding allene oxides. The product of the above reaction is unstable and is acted upon by EC 5.3.99.6, allene-oxide cyclase, to form the cyclopentenone derivative (15Z)-12-oxophyto-10,15-dienoate (OPDA), which is the first cyclic and biologically active metabolite in the jasmonate biosynthesis pathway [3]. The enzyme from many plants belongs to the CYP-74 family of P-450 monooxygenases [4].
References:
1.  Esselman, W.J. and Clagett, C.O. Products of linoleic hydroperoxide-decomposing enzyme of alfalfa seed. J. Lipid Res. 15 (1974) 173–178. [PMID: 4208994]
2.  Hamberg, M. Mechanism of corn hydroperoxide isomerase - detection of 12,13(S)-oxido-9(Z),11-octadecadienoic acid. Biochim. Biophys. Acta 920 (1987) 76–84.
3.  Hamberg, M. Biosynthesis of 12-oxo-10,15(Z)-phytodienoic acid: identification of an allene oxide cyclase. Biochem. Biophys. Res. Commun. 156 (1988) 543–550. [PMID: 3178850]
4.  Laudert, D., Pfannschmidt, U., Lottspeich, F., Holländer-Czytko, H. and Weiler, E.W. Cloning, molecular and functional characterization of Arabidopsis thaliana allene oxide synthase (CYP 74), the first enzyme of the octadecanoid pathway to jasmonates. Plant Mol. Biol. 31 (1996) 323–335. [PMID: 8756596]
[EC 4.2.1.92 created 1992, modified 2008]
 
 
EC 4.2.1.93     
Accepted name: ATP-dependent NAD(P)H-hydrate dehydratase
Reaction: (1) ATP + (6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide = ADP + phosphate + NADH
(2) ATP + (6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide phosphate = ADP + phosphate + NADPH
Glossary: (6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide = (S)-NADH-hydrate = (S)-NADHX
(6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide phosphate = (S)-NADPH-hydrate = (S)-NADPHX
Other name(s): reduced nicotinamide adenine dinucleotide hydrate dehydratase; ATP-dependent H4NAD(P)+OH dehydratase; (6S)-β-6-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine-dinucleotide hydro-lyase(ATP-hydrolysing); (6S)-6-β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine-dinucleotide hydro-lyase (ATP-hydrolysing; NADH-forming)
Systematic name: (6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine-dinucleotide hydro-lyase (ATP-hydrolysing; NADH-forming)
Comments: Acts equally well on hydrated NADH and hydrated NADPH. NAD(P)H spontaneously hydrates to both the (6S)- and (6R)- isomers, and these are interconverted by EC 5.1.99.6, NAD(P)H-hydrate epimerase, to a 60:40 ratio [4]. Hence EC 4.2.1.93 together with EC 5.1.99.6 can restore the mixture of hydrates into NAD(P)H [3,4]. The enzyme from eukaryotes has no activity with ADP, contrary to the enzyme from bacteria (cf. EC 4.2.1.136, ADP-dependent NAD(P)H-hydrate dehydratase) [4].
References:
1.  Meinhart, J.O., Chaykin, S. and Krebs, E.G. Enzymatic conversion of a reduced diphosphopyridine nucleotide derivative to reduced diphosphopyridine nucleotide. J. Biol. Chem. 220 (1956) 821–829. [PMID: 13331940]
2.  Regueiro Varela, B., Amelunxen, R. and Grisolia, S. Synthesis and degradation of monohydroxytetrahydronicotinamide adenine dinucleotide phosphate. Physiol. Chem. Phys. 2 (1970) 445–454.
3.  Acheson, S.A., Kirkman, H.N. and Wolfenden, R. Equilibrium of 5,6-hydration of NADH and mechanism of ATP-dependent dehydration. Biochemistry 27 (1988) 7371–7375. [PMID: 3061454]
4.  Marbaix, A.Y., Noel, G., Detroux, A.M., Vertommen, D., Van Schaftingen, E. and Linster, C.L. Extremely conserved ATP- or ADP-dependent enzymatic system for nicotinamide nucleotide repair. J. Biol. Chem. 286 (2011) 41246–41252. [PMID: 21994945]
[EC 4.2.1.93 created 1992, modified 2012]
 
 
EC 4.2.1.94     
Accepted name: scytalone dehydratase
Reaction: scytalone = 1,3,8-trihydroxynaphthalene + H2O
Other name(s): scytalone 7,8-hydro-lyase
Systematic name: scytalone 7,8-hydro-lyase (1,3,8-trihydroxynaphthalene-forming)
Comments: Involved, with EC 1.1.1.252 tetrahydroxynaphthalene reductase, in the biosynthesis of melanin in pathogenic fungi.
References:
1.  Butler, M.J., Lazarovits, G., Higgins, V.J. and Lachance, M.-A. Partial-purification and characterization of a dehydratase associated with the pentaketide melanogenesis pathway of Phaeococcomyces sp and other fungi. Exp. Mycol. 12 (1988) 367–376.
2.  Tajima, S., Kubo, Y., Furusawa, I. and Shishiyama, J. Purification of a melanin biosynthetic enzyme converting scytalone to 1,3,8-trihydroxynaphthalene from Cochliobolus miyabeanus. Exp. Mycol. 13 (1989) 69.
3.  Wheeler, M.H. and Greenblatt, G.A. The inhibition of melanin biosynthetic reactions in Pyricularia oryzae by compounds that prevent rice blast disease. Exp. Mycol. 12 (1988) 151–160.
[EC 4.2.1.94 created 1992]
 
 
EC 4.2.1.95     
Accepted name: kievitone hydratase
Reaction: kievitone hydrate = kievitone + H2O
Other name(s): KHase; kievitone-hydrate hydro-lyase
Systematic name: kievitone-hydrate hydro-lyase (kievitone-forming)
Comments: The enzyme from Fusarium sp. hydrates the methylbutenyl sidechain of the isoflavonoid phytoalexins, thus reducing their toxicity.
References:
1.  Turbek, C.S., Li, D., Choi, G.H., Schardl, C.L. and Smith, D.A. Induction and purification of kievitone hydratase from Fusarium solani f. sp. phaseoli. Phytochemistry 29 (1990) 2841–2846. [PMID: 1366757]
[EC 4.2.1.95 created 1992]
 
 
EC 4.2.1.96     
Accepted name: 4a-hydroxytetrahydrobiopterin dehydratase
Reaction: 4a-hydroxytetrahydrobiopterin = 6,7-dihydrobiopterin + H2O
Glossary: 4a-hydroxytetrahydrobiopterin = 6-[(1R,2S)-1,2-dihydroxypropyl]-5,6,7,8-tetrahydro-4a-hydroxypterin
6,7-dihydrobiopterin = 6-[(1R,2S)-1,2-dihydroxypropyl]-6,7-dihydropterin
Other name(s): 4α-hydroxy-tetrahydropterin dehydratase; 4a-carbinolamine dehydratase; pterin-4α-carbinolamine dehydratase; 4a-hydroxytetrahydrobiopterin hydro-lyase
Systematic name: 4a-hydroxytetrahydrobiopterin hydro-lyase (6,7-dihydrobiopterin-forming)
Comments: In concert with EC 1.5.1.34, 6,7-dihydropteridine reductase, the enzyme recycles 4a-hydroxytetrahydrobiopterin back to tetrahydrobiopterin, a cosubstrate for several enzymes, including aromatic amino acid hydroxylases. The enzyme is bifunctional, and also acts as a dimerization cofactor of hepatocyte nuclear factor-1α (HNF-1).
References:
1.  Citron, B.A., Davis, M.D., Milstien, S., Gutierrez, J., Mendel, D.B., Crabtree, G.R. and Kaufman, S. Identity of 4a-carbinolamine dehydratase, a component of the phenylalanine hydroxylation system, and DCoH, a transregulator of homeodomain proteins. Proc. Natl. Acad. Sci. USA 89 (1992) 11891–11894. [PMID: 1465414]
2.  Hauer, C.R., Rebrin, I., Thöny, B., Neuheiser, F., Curtius, H.C., Hunziker, P., Blau, N., Ghisla, S., Heizmann, C.W. Phenylalanine hydroxylase-stimulating protein: pterin-4α-carbinolamine dehydratase from rat and human liver. J. Biol. Chem. 268 (1993) 4828–4831. [PMID: 8444860]
3.  Thony, B., Neuheiser, F., Blau, N. and Heizmann, C.W. Characterization of the human PCBD gene encoding the bifunctional protein pterin-4 α-carbinolamine dehydratase/dimerization cofactor for the transcription factor HNF-1 α. Biochem. Biophys. Res. Commun. 210 (1995) 966–973. [PMID: 7763270]
4.  Endrizzi, J.A., Cronk, J.D., Wang, W., Crabtree, G.R. and Alber, T. Crystal structure of DCoH, a bifunctional, protein-binding transcriptional coactivator. Science 268 (1995) 556–559. [PMID: 7725101]
5.  Cronk, J.D., Endrizzi, J.A. and Alber, T. High-resolution structures of the bifunctional enzyme and transcriptional coactivator DCoH and its complex with a product analogue. Protein Sci. 5 (1996) 1963–1972. [PMID: 8897596]
[EC 4.2.1.96 created 1999, modified 2020]
 
 
EC 4.2.1.97     
Accepted name: phaseollidin hydratase
Reaction: phaseollidin hydrate = phaseollidin + H2O
Other name(s): phaseollidin-hydrate hydro-lyase
Systematic name: phaseollidin-hydrate hydro-lyase (phaseollidin-forming)
Comments: The enzyme from Fusarium solani, which is distinct from kievitone hydratase (EC 4.2.1.95), hydrates the methylbutenyl side-chain of the isoflavonoid phytoalexin, phaseollidin.
References:
1.  Turbek, C.S., Smith, D.A., Schardl, C.L. An extracellular enzyme from Fusarium solani f.sp. phaseoli, which catalyses hydration of the isoflavonoid phytoalexin, phaseollidin. FEMS Microbiol. Lett. 94 (1992) 187–190. [PMID: 1521768]
[EC 4.2.1.97 created 1999]
 
 
EC 4.2.1.98     
Accepted name: 16α-hydroxyprogesterone dehydratase
Reaction: 16α-hydroxyprogesterone = 16,17-didehydroprogesterone + H2O
Other name(s): hydroxyprogesterone dehydroxylase; 16α-hydroxyprogesterone dehydroxylase; 16α-dehydroxylase; 16α-hydroxyprogesterone hydro-lyase
Systematic name: 16α-hydroxyprogesterone hydro-lyase (16,17-didehydroprogesterone-forming)
Comments: 16α-Hydroxypregnenolone is also a substrate.
References:
1.  Glass, T.L. and Lamppa, R.S. Purification and properties of 16α-hydroxyprogesterone dehydroxylase from Eubacterium sp. strain 144. Biochim. Biophys. Acta 837 (1985) 103–110. [PMID: 4052439]
[EC 4.2.1.98 created 1999, modified 2004 (EC 4.2.1.86 created 1989, incorporated 2004)]
 
 
EC 4.2.1.99     
Accepted name: 2-methylisocitrate dehydratase
Reaction: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = (Z)-but-2-ene-1,2,3-tricarboxylate + H2O
Glossary: cis-2-methylaconitate = (Z)-but-2-ene-1,2,3-tricarboxylate
(2S,3R)-2-methylisocitrate = (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = threo-Ds-2-methylisocitrate
Other name(s): (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate hydro-lyase
Systematic name: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate hydro-lyase [(Z)-but-2-ene-1,2,3-tricarboxylate-forming]
Comments: The enzyme from the fungus Yarrowia lipolytica (Saccharomycopsis) does not act on isocitrate.
References:
1.  Aoki, H., Uchiyama, H., Umetsu, H., Tabuchi, T. Isolation of 2-methylisocitrate dehydratase, a new enzyme serving in the methylcitric acid cycle for propionate metabolism, from Yarrowia lipolytica. Biosci. Biotechnol. Biochem. 59 (1995) 1825–1828.
2.  Tabuchi, T., Umetsu, H., Aoki, H., Uchiyama, H. Characteristics of 2-methylisocitrate dehydratase, isolated from Yarrowia lipolytica, in comparison to aconitase. Biosci. Biotechnol. Biochem. 59 (1995) 2013–2017.
[EC 4.2.1.99 created 1999]
 
 
EC 4.2.1.100     
Accepted name: cyclohexa-1,5-dienecarbonyl-CoA hydratase
Reaction: 6-hydroxycyclohex-1-ene-1-carbonyl-CoA = cyclohexa-1,5-diene-1-carbonyl-CoA + H2O
Other name(s): cyclohexa-1,5-diene-1-carbonyl-CoA hydratase; dienoyl-CoA hydratase; cyclohexa-1,5-dienecarbonyl-CoA hydro-lyase (incorrect); 6-hydroxycyclohex-1-enecarbonyl-CoA hydro-lyase (cyclohexa-1,5-dienecarbonyl-CoA-forming)
Systematic name: 6-hydroxycyclohex-1-ene-1-carbonyl-CoA hydro-lyase (cyclohexa-1,5-diene-1-carbonyl-CoA-forming)
Comments: Forms part of the anaerobic benzoate degradation pathway, which also includes EC 1.3.8.6 [glutaryl-CoA dehydrogenase (ETF)], EC 1.3.7.8 (benzoyl-CoA reductase) and EC 4.2.1.55 (3-hydroyxbutyryl-CoA dehydratase).
References:
1.  Laempe, D., Eisenreich, W., Bacher, A. and Fuchs, G. Cyclohexa-1,5-diene-1-carboxyl-CoA hydratase, an enzyme involved in anaerobic metabolism of benzoyl-CoA in the denitrifying bacterium Thauera aromatica. Eur. J. Biochem. 255 (1998) 618–627. [PMID: 9738901]
2.  Harwood, C.S. and Gibson, J. Shedding light on anaerobic benzene ring degradation: a process unique to prokaryotes? J. Bacteriol. 179 (1997) 301–309. [PMID: 8990279]
3.  Koch, J., Eisenreich, W., Bacher, A. and Fuchs, G. Products of enzymatic reduction of benzoyl-CoA, a key reaction in anaerobic aromatic metabolism. Eur. J. Biochem. 211 (1993) 649–661. [PMID: 8436125]
[EC 4.2.1.100 created 2000, modified 2001]
 
 
EC 4.2.1.101      
Transferred entry: trans-feruloyl-CoA hydratase. Now included with EC 4.1.2.61, feruloyl-CoA hydratase/lyase
[EC 4.2.1.101 created 2000, deleted 2020]
 
 
EC 4.2.1.102      
Transferred entry: cyclohexa-1,5-dienecarbonyl-CoA hydratase. Now EC 4.2.1.100, cyclohexa-1,5-dienecarbonyl-CoA hydratase
[EC 4.2.1.102 created 2001, deleted 2001]
 
 
EC 4.2.1.103     
Accepted name: cyclohexyl-isocyanide hydratase
Reaction: N-cyclohexylformamide = cyclohexyl isocyanide + H2O
Other name(s): isonitrile hydratase; N-cyclohexylformamide hydro-lyase
Systematic name: N-cyclohexylformamide hydro-lyase (cyclohexyl-isocyanide-forming)
Comments: The enzyme from Pseudomonas putida strain N19-2 can also catalyse the hydration of other isonitriles to the corresponding N-substituted formamides. The enzyme has no metal requirements.
References:
1.  Goda, M., Hashimoto, Y., Shimizu, S. and Kobayashi, M. Discovery of a novel enzyme, isonitrile hydratase, involved in nitrogen-carbon triple bond cleavage. J. Biol. Chem. 276 (2001) 23480–23485. [PMID: 11306561]
[EC 4.2.1.103 created 2001]
 
 
EC 4.2.1.104     
Accepted name: cyanase
Reaction: cyanate + HCO3- + 2 H+ = NH3 + 2 CO2 (overall reaction)
(1a) cyanate + HCO3- + H+ = carbamate + CO2
(1b) carbamate + H+ = NH3 + CO2 (spontaneous)
Glossary: cyanate = NCO-
carbamate = H2N-CO-O-
Other name(s): cyanate lyase; cyanate hydrolase; cyanate aminohydrolase; cyanate C-N-lyase; cyanate hydratase
Systematic name: carbamate hydro-lyase
Comments: This enzyme, which is found in bacteria and plants, is used to decompose cyanate, which can be used as the sole source of nitrogen [6,7]. Reaction (1) can be considered as the reverse of ’carbamate = cyanate + H2O′, where this is assisted by reaction with bicarbonate and carbon dioxide (see mechanism above) [2], and hence is classified in sub-subclass 4.2.1. Bicarbonate functions as a recycling substrate [2].
References:
1.  Anderson, P.M. Purification and properties of the inducible enzyme cyanase. Biochemistry 19 (1980) 2882–2888. [PMID: 6994799]
2.  Johnson, W.V. and Anderson, P.M. Bicarbonate is a recycling substrate for cyanase. J. Biol. Chem. 262 (1987) 9021–9025. [PMID: 3110153]
3.  Taussig, A. The synthesis of the induced enzyme, "cyanase", in E. coli. Biochim. Biophys. Acta 44 (1960) 510–519. [PMID: 13775509]
4.  Taussig, A. Some properties of the induced enzyme cyanase. Can. J. Biochem. 43 (1965) 1063–1069. [PMID: 5322950]
5.  Anderson, P.M., Korte, J.J. and Holcomb, T.A. Reaction of the N-terminal methionine residues in cyanase with diethylpyrocarbonate. Biochemistry 33 (1994) 14121–14125. [PMID: 7947823]
6.  Kozliak, E.I., Fuchs, J.A., Guilloton, M.B. and Anderson, P.M. Role of bicarbonate/CO2 in the inhibition of Escherichia coli growth by cyanate. J. Bacteriol. 177 (1995) 3213–3219. [PMID: 7768821]
7.  Walsh, M.A., Otwinowski, Z., Perrakis, A., Anderson, P.M. and Joachimiak, A. Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site. Structure 8 (2000) 505–514. [PMID: 10801492]
[EC 4.2.1.104 created 1972 as EC 3.5.5.3, transferred 1990 to EC 4.3.99.1, transferred 2001 to EC 4.2.1.104, modified 2007]
 
 
EC 4.2.1.105     
Accepted name: 2-hydroxyisoflavanone dehydratase
Reaction: (1) 2,4′,7-trihydroxyisoflavanone = daidzein + H2O
(2) 2,4′,5,7-tetrahydroxyisoflavanone = genistein + H2O
Glossary: daidzein = 4′,7-dihydroxyisoflavone
genistein = 4′,5,7-dihydroxyisoflavone
Other name(s): 2,7,4′-trihydroxyisoflavanone hydro-lyase; 2,7,4′-trihydroxyisoflavanone hydro-lyase (daidzein-forming)
Systematic name: 2,4′,7-trihydroxyisoflavanone hydro-lyase (daidzein-forming)
Comments: Catalyses the final step in the formation of the isoflavonoid skeleton. The reaction also occurs spontaneously.
References:
1.  Hakamatsuka, T., Mori, K., Ishida, S., Ebizuka, Y and Sankawa, U. Purification of 2-hydroxyisoflavanone dehydratase from the cell cultures of Pueraria lobata. Phytochemistry 49 (1998) 497–505.
[EC 4.2.1.105 created 2004, modified 2013]
 
 
EC 4.2.1.106     
Accepted name: bile-acid 7α-dehydratase
Reaction: 7α,12α-dihydroxy-3-oxochol-4-en-24-oyl-CoA = 12α-hydroxy-3-oxochola-4,6-dien-24-oyl-CoA + H2O
Other name(s): baiE (gene name); 7α,12α-dihydroxy-3-oxochol-4-enoate hydro-lyase; 7α,12α-dihydroxy-3-oxochol-4-enoate hydro-lyase (12α-hydroxy-3-oxochola-4,6-dienoate-forming); BA7 α dehydratase
Systematic name: 7α,12α-dihydroxy-3-oxochol-4-enoyl-CoA hydro-lyase (12α-hydroxy-3-oxochola-4,6-dienoyl-CoA-forming)
Comments: This enzyme, characterized from the gut bacterium Clostridium scindens (previously known as Eubacterium sp. strain VPI 12708), participates in the 7-dehydroxylation process associated with bile acid degradation.
References:
1.  Mallonee, D.H., White, W.B. and Hylemon, P.B. Cloning and sequencing of a bile acid-inducible operon from Eubacterium sp. strain VPI 12708. J. Bacteriol. 172 (1990) 7011–7019. [PMID: 2254270]
2.  Dawson, J.A., Mallonee, D.H., Björkhem, I. and Hylemon, P.B. Expression and characterization of a C24 bile acid 7α-dehydratase from Eubacterium sp. strain VPI 12708 in Escherichia coli. J. Lipid Res. 37 (1996) 1258–1267. [PMID: 8808760]
3.  Bhowmik, S., Chiu, H.P., Jones, D.H., Chiu, H.J., Miller, M.D., Xu, Q., Farr, C.L., Ridlon, J.M., Wells, J.E., Elsliger, M.A., Wilson, I.A., Hylemon, P.B. and Lesley, S.A. Structure and functional characterization of a bile acid 7α dehydratase BaiE in secondary bile acid synthesis. Proteins 84 (2016) 316–331. [PMID: 26650892]
[EC 4.2.1.106 created 2005, modified 2016]
 
 
EC 4.2.1.107     
Accepted name: 3α,7α,12α-trihydroxy-5β-cholest-24-enoyl-CoA hydratase
Reaction: (24R,25R)-3α,7α,12α,24-tetrahydroxy-5β-cholestanoyl-CoA = (24E)-3α,7α,12α-trihydroxy-5β-cholest-24-enoyl-CoA + H2O
Other name(s): 46 kDa hydratase 2; (24R,25R)-3α,7α,12α,24-tetrahydroxy-5β-cholestanoyl-CoA hydro-lyase
Systematic name: (24R,25R)-3α,7α,12α,24-tetrahydroxy-5β-cholestanoyl-CoA hydro-lyase [(24E)-3α,7α,12α-trihydroxy-5β-cholest-24-enoyl-CoA-forming]
Comments: This enzyme forms part of the rat peroxisomal multifunctional enzyme perMFE-2, which also exhibits a dehydrogenase activity. The enzyme is involved in the β-oxidation of the cholesterol side chain in the cholic-acid-biosynthesis pathway.
References:
1.  Qin, Y.M., Haapalainen, A.M., Conry, D., Cuebas, D.A., Hiltunen, J.K. and Novikov, D.K. Recombinant 2-enoyl-CoA hydratase derived from rat peroxisomal multifunctional enzyme 2: role of the hydratase reaction in bile acid synthesis. Biochem. J. 328 (1997) 377–382. [PMID: 9371691]
2.  Xu, R. and Cuebas, D.A. The reactions catalyzed by the inducible bifunctional enzyme of rat liver peroxisomes cannot lead to the formation of bile acids. Biochem. Biophys. Res. Commun. 221 (1996) 271–278. [PMID: 8619845]
3.  Kinoshita, T., Miyata, M., Ismail, S.M., Fujimoto, Y., Kakinuma, K., Kokawa, N.I. and Morisaki, M. Synthesis and determination of stereochemistry of four diastereoisomers at the C-24 and C-25 positions of 3α,7α,12α,24-tetrahydroxy-5β-cholestan-26-oic acid and cholic acid. Chem. Pharm. Bull. 36 (1988) 134–141.
4.  Fujimoto, Y., Kinoshita, T., Oya, I., Kakinuma, K., Ismail, S.M., Sonoda, Y., Sato, Y. and Morisaki, M. Non-stereoselective conversion of the four diastereoisomers at the C-24 and C-25 positions of 3α,7α,12α,24-tetrahydroxy-5β-cholestan-26-oic acid and cholic acid. Chem. Pharm. Bull. 36 (1988) 142–145.
5.  Kurosawa, T., Sato, M., Nakano, H., Fujiwara, M., Murai, T., Yoshimura, T. and Hashimoto, T. Conjugation reactions catalyzed by bifunctional proteins related to β-oxidation in bile acid biosynthesis. Steroids 66 (2001) 107–114. [PMID: 11146090]
6.  Russell, D.W. The enzymes, regulation, and genetics of bile acid synthesis. Annu. Rev. Biochem. 72 (2003) 137–174. [PMID: 12543708]
[EC 4.2.1.107 created 2005]
 
 
EC 4.2.1.108     
Accepted name: ectoine synthase
Reaction: (2S)-4-acetamido-2-aminobutanoate = L-ectoine + H2O
Glossary: ectoine = (4S)-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylate
Other name(s): ectC (gene name); N-acetyldiaminobutyrate dehydratase; N-acetyldiaminobutanoate dehydratase; L-ectoine synthase; 4-N-acetyl-L-2,4-diaminobutanoate hydro-lyase (L-ectoine-forming); N4-acetyl-L-2,4-diaminobutanoate hydro-lyase (L-ectoine-forming)
Systematic name: (2S)-4-acetamido-2-aminobutanoate (L-ectoine-forming)
Comments: Ectoine is an osmoprotectant that is found in halophilic eubacteria. This enzyme is part of the ectoine biosynthesis pathway and only acts in the direction of ectoine formation. cf. EC 3.5.4.44, ectoine hydrolase.
References:
1.  Peters, P., Galinski, E.A. and Truper, H.G. The biosynthesis of ectoine. FEMS Microbiol. Lett. 71 (1990) 157–162.
2.  Ono, H., Sawada, K., Khunajakr, N., Tao, T., Yamamoto, M., Hiramoto, M., Shinmyo, A., Takano, M. and Murooka, Y. Characterization of biosynthetic enzymes for ectoine as a compatible solute in a moderately halophilic eubacterium, Halomonas elongata. J. Bacteriol. 181 (1999) 91–99. [PMID: 9864317]
3.  Kuhlmann, A.U. and Bremer, E. Osmotically regulated synthesis of the compatible solute ectoine in Bacillus pasteurii and related Bacillus spp. Appl. Environ. Microbiol. 68 (2002) 772–783. [PMID: 11823218]
4.  Louis, P. and Galinski, E.A. Characterization of genes for the biosynthesis of the compatible solute ectoine from Marinococcus halophilus and osmoregulated expression in Escherichia coli. Microbiology 143 (1997) 1141–1149. [PMID: 9141677]
5.  Schwibbert, K., Marin-Sanguino, A., Bagyan, I., Heidrich, G., Lentzen, G., Seitz, H., Rampp, M., Schuster, S.C., Klenk, H.P., Pfeiffer, F., Oesterhelt, D. and Kunte, H.J. A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581 T. Environ. Microbiol. 13 (2011) 1973–1994. [PMID: 20849449]
[EC 4.2.1.108 created 2006, modified 2017]
 
 
EC 4.2.1.109     
Accepted name: methylthioribulose 1-phosphate dehydratase
Reaction: 5-(methylsulfanyl)-D-ribulose 1-phosphate = 5-(methylsulfanyl)-2,3-dioxopentyl phosphate + H2O
Other name(s): 1-PMT-ribulose dehydratase; S-methyl-5-thio-D-ribulose-1-phosphate hydro-lyase; S-methyl-5-thio-D-ribulose-1-phosphate 4-hydro-lyase [5-(methylthio)-2,3-dioxopentyl-phosphate-forming]
Systematic name: 5-(methylsulfanyl)-D-ribulose-1-phosphate 4-hydro-lyase [5-(methylsulfanyl)-2,3-dioxopentyl-phosphate-forming]
Comments: This enzyme forms part of the methionine-salvage pathway.
References:
1.  Furfine, E.S. and Abeles, R.H. Intermediates in the conversion of 5′-S-methylthioadenosine to methionine in Klebsiella pneumoniae. J. Biol. Chem. 263 (1988) 9598–9606. [PMID: 2838472]
2.  Wray, J.W. and Abeles, R.H. The methionine salvage pathway in Klebsiella pneumoniae and rat liver. Identification and characterization of two novel dioxygenases. J. Biol. Chem. 270 (1995) 3147–3153. [PMID: 7852397]
[EC 4.2.1.109 created 2006]
 
 
EC 4.2.1.110     
Accepted name: aldos-2-ulose dehydratase
Reaction: 1,5-anhydro-D-fructose = 2-hydroxy-2-(hydroxymethyl)-2H-pyran-3(6H)-one + H2O (overall reaction)
(1a) 1,5-anhydro-D-fructose = 1,5-anhydro-4-deoxy-D-glycero-hex-3-en-2-ulose + H2O
(1b) 1,5-anhydro-4-deoxy-D-glycero-hex-3-en-2-ulose = 2-hydroxy-2-(hydroxymethyl)-2H-pyran-3(6H)-one
Glossary: 1,5-anhydro-D-fructose = 1,5-anhydro-D-arabino-hex-2-ulose = (4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)dihydro-2H-pyran-3(4H)-one
ascopyrone M = 1,5-anhydro-4-deoxy-D-glycero-hex-3-en-2-ulose = (6S)-4-hydroxy-6-(hydroxymethyl)-2H-pyran-3(6H)-one
microthecin = 2-hydroxy-2-(hydroxymethyl)-2H-pyran-3(6H)-one
Other name(s): pyranosone dehydratase; AUDH; 1,5-anhydro-D-fructose dehydratase (microthecin-forming)
Systematic name: 1,5-anhydro-D-fructose hydro-lyase (microthecin-forming)
Comments: This enzyme catalyses two of the steps in the anhydrofructose pathway, which leads to the degradation of glycogen and starch via 1,5-anhydro-D-fructose [1,2]. Aldose-2-uloses such as 2-dehydroglucose can also act as substrates, but more slowly [1,2,4]. This is a bifunctional enzyme that acts as both a lyase and as an isomerase [2]. Differs from EC 4.2.1.111, which can carry out only reaction (1a), is inhibited by its product and requires metal ions for activity [1].
References:
1.  Yu, S. and Fiskesund, R. The anhydrofructose pathway and its possible role in stress response and signaling. Biochim. Biophys. Acta 1760 (2006) 1314–1322. [PMID: 16822618]
2.  Yu, S. Enzymatic description of the anhydrofructose pathway of glycogen degradation. II. Gene identification and characterization of the reactions catalyzed by aldos-2-ulose dehydratase that converts 1,5-anhydro-D-fructose to microthecin with ascopyrone M as the intermediate. Biochim. Biophys. Acta 1723 (2005) 63–73. [PMID: 15716041]
3.  Broberg, A., Kenne, L. and Pedersén, M. Presence of microthecin in the red alga Gracilariopsis lemaneiformis and its formation from 1,5-anhydro-D-fructose. Phytochemistry 41 (1996) 151–154.
4.  Gabriel, J., Volc, J., Sedmera, P., Daniel, G. and Kubátová, E. Pyranosone dehydratase from the basidiomycete Phanerochaete chrysosporium: improved purification, and identification of 6-deoxy-D-glucosone and D-xylosone reaction products. Arch. Microbiol. 160 (1993) 27–34. [PMID: 8352649]
5.  Yu, S., Refdahl, C. and Lundt, I. Enzymatic description of the anhydrofructose pathway of glycogen degradation; I. Identification and purification of anhydrofructose dehydratase, ascopyrone tautomerase and α-1,4-glucan lyase in the fungus Anthracobia melaloma. Biochim. Biophys. Acta 1672 (2004) 120–129. [PMID: 15110094]
[EC 4.2.1.110 created 2006]
 
 
EC 4.2.1.111     
Accepted name: 1,5-anhydro-D-fructose dehydratase
Reaction: 1,5-anhydro-D-fructose = 1,5-anhydro-4-deoxy-D-glycero-hex-3-en-2-ulose + H2O
Glossary: 1,5-anhydro-D-fructose = 1,5-anhydro-D-arabino-hex-2-ulose = (4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)dihydro-2H-pyran-3(4H)-one
ascopyrone M = 1,5-anhydro-4-deoxy-D-glycero-hex-3-en-2-ulose = (6S)-4-hydroxy-6-(hydroxymethyl)-2H-pyran-3(6H)-one
Other name(s): 1,5-anhydro-D-fructose 4-dehydratase; 1,5-anhydro-D-fructose hydrolyase; 1,5-anhydro-D-arabino-hex-2-ulose dehydratase; AFDH; AF dehydratase; 1,5-anhydro-D-fructose hydro-lyase
Systematic name: 1,5-anhydro-D-fructose hydro-lyase (ascopyrone-M-forming)
Comments: This enzyme catalyses one of the steps in the anhydrofructose pathway, which leads to the degradation of glycogen and starch via 1,5-anhydro-D-fructose [1,2]. The other enzymes involved in this pathway are EC 4.2.1.110 (aldos-2-ulose dehydratase), EC 4.2.2.13 [exo-(1→4)-α-D-glucan lyase] and EC 5.3.2.7 (ascopyrone tautomerase). Requires divalent (Ca2+ or Mg2+) or monovalent cations (Na+) for optimal activity. Unlike EC 4.2.1.110, the enzyme is specific for 1,5-anhydro-D-fructose as substrate and shows no activity towards aldose-2-uloses such as 2-dehydroglucose [1,2,3]. In addition, it is inhibited by its end-product ascopyrone M [2] and it cannot convert ascopyrone M into microthecin, as can EC 4.2.1.110.
References:
1.  Yu, S., Refdahl, C. and Lundt, I. Enzymatic description of the anhydrofructose pathway of glycogen degradation; I. Identification and purification of anhydrofructose dehydratase, ascopyrone tautomerase and α-1,4-glucan lyase in the fungus Anthracobia melaloma. Biochim. Biophys. Acta 1672 (2004) 120–129. [PMID: 15110094]
2.  Yu, S. and Fiskesund, R. The anhydrofructose pathway and its possible role in stress response and signaling. Biochim. Biophys. Acta 1760 (2006) 1314–1322. [PMID: 16822618]
3.  Yu, S. Enzymatic description of the anhydrofructose pathway of glycogen degradation. II. Gene identification and characterization of the reactions catalyzed by aldos-2-ulose dehydratase that converts 1,5-anhydro-D-fructose to microthecin with ascopyrone M as the intermediate. Biochim. Biophys. Acta 1723 (2005) 63–73. [PMID: 15716041]
[EC 4.2.1.111 created 2006]
 
 
EC 4.2.1.112     
Accepted name: acetylene hydratase
Reaction: acetaldehyde = acetylene + H2O
Other name(s): AH; acetaldehyde hydro-lyase
Systematic name: acetaldehyde hydro-lyase (acetylene-forming)
Comments: This is a non-redox-active enzyme that contains two molybdopterin guanine dinucleotide (MGD) cofactors, a tungsten centre and a cubane type [4Fe-4S] cluster [2].The tungsten centre binds a water molecule that is activated by an adjacent aspartate residue, enabling it to attack acetylene bound in a distinct hydrophobic pocket [2]. Ethylene cannot act as a substrate [1].
References:
1.  Rosner, B.M. and Schink, B. Purification and characterization of acetylene hydratase of Pelobacter acetylenicus, a tungsten iron-sulfur protein. J. Bacteriol. 177 (1995) 5767–5772. [PMID: 7592321]
2.  Seiffert, G.B., Ullmann, G.M., Messerschmidt, A., Schink, B., Kroneck, P.M. and Einsle, O. Structure of the non-redox-active tungsten/[4Fe:4S] enzyme acetylene hydratase. Proc. Natl. Acad. Sci. USA 104 (2007) 3073–3077. [PMID: 17360611]
[EC 4.2.1.112 created 2007]
 
 
EC 4.2.1.113     
Accepted name: o-succinylbenzoate synthase
Reaction: (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate + H2O
Glossary: 2-succinylbenzoate = o-succinylbenzoate = 4-(2-carboxyphenyl)-4-oxobutanoate
Other name(s): o-succinylbenzoic acid synthase; OSB synthase; OSBS; 2-succinylbenzoate synthase; MenC
Systematic name: (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate hydro-lyase (2-succinylbenzoate-forming)
Comments: Belongs to the enolase superfamily and requires divalent cations, preferably Mg2+ or Mn2+, for activity. Forms part of the vitamin-K-biosynthesis pathway.
References:
1.  Sharma, V., Meganathan, R. and Hudspeth, M.E. Menaquinone (vitamin K2) biosynthesis: cloning, nucleotide sequence, and expression of the menC gene from Escherichia coli. J. Bacteriol. 175 (1993) 4917–4921. [PMID: 8335646]
2.  Klenchin, V.A., Taylor Ringia, E.A., Gerlt, J.A. and Rayment, I. Evolution of enzymatic activity in the enolase superfamily: structural and mutagenic studies of the mechanism of the reaction catalyzed by o-succinylbenzoate synthase from Escherichia coli. Biochemistry 42 (2003) 14427–14433. [PMID: 14661953]
3.  Palmer, D.R., Garrett, J.B., Sharma, V., Meganathan, R., Babbitt, P.C. and Gerlt, J.A. Unexpected divergence of enzyme function and sequence: "N-acylamino acid racemase" is o-succinylbenzoate synthase. Biochemistry 38 (1999) 4252–4258. [PMID: 10194342]
4.  Thompson, T.B., Garrett, J.B., Taylor, E.A., Meganathan, R., Gerlt, J.A. and Rayment, I. Evolution of enzymatic activity in the enolase superfamily: structure of o-succinylbenzoate synthase from Escherichia coli in complex with Mg2+ and o-succinylbenzoate. Biochemistry 39 (2000) 10662–10676. [PMID: 10978150]
5.  Taylor Ringia, E.A., Garrett, J.B., Thoden, J.B., Holden, H.M., Rayment, I. and Gerlt, J.A. Evolution of enzymatic activity in the enolase superfamily: functional studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis. Biochemistry 43 (2004) 224–229. [PMID: 14705949]
[EC 4.2.1.113 created 2007]
 
 
EC 4.2.1.114     
Accepted name: methanogen homoaconitase
Reaction: (R)-2-hydroxybutane-1,2,4-tricarboxylate = (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate (overall reaction)
(1a) (R)-2-hydroxybutane-1,2,4-tricarboxylate = (Z)-but-1-ene-1,2,4-tricarboxylate + H2O
(1b) (Z)-but-1-ene-1,2,4-tricarboxylate + H2O = (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate
Glossary: cis-homoaconitate = (Z)-but-1-ene-1,2,4-tricarboxylate
(R)-homocitrate = (R)-2-hydroxybutane-1,2,4-tricarboxylate
homoisocitrate = (-)-threo-homoisocitrate = (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate
Other name(s): methanogen HACN
Systematic name: (R)-2-hydroxybutane-1,2,4-tricarboxylate hydro-lyase [(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate-forming]
Comments: This enzyme catalyses several reactions in the pathway of coenzyme-B biosynthesis in methanogenic archaea. Requires a [4Fe-4S] cluster for activity. In contrast to EC 4.2.1.36, homoaconitate hydratase, this enzyme can catalyse both the dehydration of (R)-homocitrate to form cis-homoaconitate and the subsequent hydration reaction that forms homoisocitrate. In addition to cis-homoaconitate, the enzyme can also catalyse the hydration of the physiological substrates dihomocitrate and trihomocitrate as well as the non-physiological substrate tetrahomocitrate. cis-Aconitate and threo-DL-isocitrate cannot act as substrates, and (S)-homocitrate and trans-homoaconitate act as inhibitors of the enzyme.
References:
1.  Drevland, R.M., Jia, Y., Palmer, D.R. and Graham, D.E. Methanogen homoaconitase catalyzes both hydrolyase reactions in coenzyme B biosynthesis. J. Biol. Chem. 283 (2008) 28888–28896. [PMID: 18765671]
[EC 4.2.1.114 created 2009]
 
 
EC 4.2.1.115     
Accepted name: UDP-N-acetylglucosamine 4,6-dehydratase (configuration-inverting)
Reaction: UDP-N-acetyl-α-D-glucosamine = UDP-2-acetamido-2,6-dideoxy-β-L-arabino-hex-4-ulose + H2O
Glossary: pseudaminic acid = 5,7-bis(acetylamino)-3,5,7,9-tetradeoxy-L-glycero-α-L-manno-2-nonulopyranosonic acid
Other name(s): FlaA1; UDP-N-acetylglucosamine 5-inverting 4,6-dehydratase; PseB; UDP-N-acetylglucosamine hydro-lyase (inverting; UDP-2-acetamido-2,6-dideoxy-β-L-arabino-hex-4-ulose-forming)
Systematic name: UDP-N-acetyl-α-D-glucosamine hydro-lyase (inverting; UDP-2-acetamido-2,6-dideoxy-β-L-arabino-hex-4-ulose-forming)
Comments: Contains NADP+ as a cofactor. This is the first enzyme in the biosynthetic pathway of pseudaminic acid [3], a sialic-acid-like sugar that is unique to bacteria and is used by Helicobacter pylori to modify its flagellin. This enzyme plays a critical role in H. pylori’s pathogenesis, being involved in the synthesis of both functional flagella and lipopolysaccharides [1,2]. It is completely inhibited by UDP-α-D-galactose. The reaction results in the chirality of the C-5 atom being inverted. It is thought that Lys-133 acts sequentially as a catalytic acid, protonating the C-6 hydroxy group and as a catalytic base, abstracting the C-5 proton, resulting in the elimination of water. This enzyme belongs to the short-chain dehydrogenase/reductase family of enzymes.
References:
1.  Ishiyama, N., Creuzenet, C., Miller, W.L., Demendi, M., Anderson, E.M., Harauz, G., Lam, J.S. and Berghuis, A.M. Structural studies of FlaA1 from Helicobacter pylori reveal the mechanism for inverting 4,6-dehydratase activity. J. Biol. Chem. 281 (2006) 24489–24495. [PMID: 16651261]
2.  Schirm, M., Soo, E.C., Aubry, A.J., Austin, J., Thibault, P. and Logan, S.M. Structural, genetic and functional characterization of the flagellin glycosylation process in Helicobacter pylori. Mol. Microbiol. 48 (2003) 1579–1592. [PMID: 12791140]
3.  Schoenhofen, I.C., McNally, D.J., Brisson, J.R. and Logan, S.M. Elucidation of the CMP-pseudaminic acid pathway in Helicobacter pylori: synthesis from UDP-N-acetylglucosamine by a single enzymatic reaction. Glycobiology 16 (2006) 8C–14C. [PMID: 16751642]
[EC 4.2.1.115 created 2009]
 
 
EC 4.2.1.116     
Accepted name: 3-hydroxypropionyl-CoA dehydratase
Reaction: 3-hydroxypropanoyl-CoA = acryloyl-CoA + H2O
Glossary: acryloyl-CoA = acrylyl-CoA
3-hydroxypropanoyl-CoA = 3-hydroxypropionyl-CoA
Other name(s): 3-hydroxypropionyl-CoA hydro-lyase; 3-hydroxypropanoyl-CoA dehydratase
Systematic name: 3-hydroxypropanoyl-CoA hydro-lyase
Comments: Catalyses a step in the 3-hydroxypropanoate/4-hydroxybutanoate cycle, an autotrophic CO2 fixation pathway found in some thermoacidophilic archaea [1]. The enzyme from Metallosphaera sedula acts nearly equally as well on (S)-3-hydroxybutanoyl-CoA but not (R)-3-hydroxybutanoyl-CoA [2].
References:
1.  Berg, I.A., Kockelkorn, D., Buckel, W. and Fuchs, G. A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea. Science 318 (2007) 1782–1786. [PMID: 18079405]
2.  Teufel, R., Kung, J.W., Kockelkorn, D., Alber, B.E. and Fuchs, G. 3-hydroxypropionyl-coenzyme A dehydratase and acryloyl-coenzyme A reductase, enzymes of the autotrophic 3-hydroxypropionate/4-hydroxybutyrate cycle in the Sulfolobales. J. Bacteriol. 191 (2009) 4572–4581. [PMID: 19429610]
[EC 4.2.1.116 created 2009]
 
 
EC 4.2.1.117     
Accepted name: 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
Reaction: (2S,3S)-2-methylcitrate = 2-methyl-trans-aconitate + H2O
Glossary: (2S,3S)-2-methylcitrate = (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate
2-methyl-trans-aconitate = (2E)-but-2-ene-1,2,3-tricarboxylate
Systematic name: (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate hydro-lyase (2-methyl-trans-aconitate forming)
Comments: Catalyses the dehydration of (2S,3S)-2-methylcitrate, forming the trans isomer of 2-methyl-aconitate (unlike EC 4.2.1.79, which forms only the cis isomer). Part of a propionate degradation pathway. The enzyme from Shewanella oneidensis can also accept citrate and cis-aconitate, but activity with (2S,3S)-2-methylcitrate was approximately 2.5-fold higher. 2-methylisocitrate and isocitrate were not substrates [1]. An iron-sulfur protein.
References:
1.  Grimek, T.L. and Escalante-Semerena, J.C. The acnD genes of Shewenella oneidensis and Vibrio cholerae encode a new Fe/S-dependent 2-methylcitrate dehydratase enzyme that requires prpF function in vivo. J. Bacteriol. 186 (2004) 454–462. [PMID: 14702315]
[EC 4.2.1.117 created 2009]
 
 
EC 4.2.1.118     
Accepted name: 3-dehydroshikimate dehydratase
Reaction: 3-dehydro-shikimate = 3,4-dihydroxybenzoate + H2O
Glossary: 3,4-dihydroxybenzoate = protocatechuate
Systematic name: 3-dehydroshikimate hydro-lyase
Comments: Catalyses an early step in the biosynthesis of petrobactin, a siderophore produced by many bacteria, including the human pathogen Bacillus anthracis. Requires divalent ions, with a preference for Mn2+.
References:
1.  Fox, D.T., Hotta, K., Kim, C.Y. and Koppisch, A.T. The missing link in petrobactin biosynthesis: asbF encodes a (-)-3-dehydroshikimate dehydratase. Biochemistry 47 (2008) 12251–12253. [PMID: 18975921]
2.  Pfleger, B.F., Kim, Y., Nusca, T.D., Maltseva, N., Lee, J.Y., Rath, C.M., Scaglione, J.B., Janes, B.K., Anderson, E.C., Bergman, N.H., Hanna, P.C., Joachimiak, A. and Sherman, D.H. Structural and functional analysis of AsbF: origin of the stealth 3,4-dihydroxybenzoic acid subunit for petrobactin biosynthesis. Proc. Natl. Acad. Sci. USA 105 (2008) 17133–17138. [PMID: 18955706]
[EC 4.2.1.118 created 2009]
 
 
EC 4.2.1.119     
Accepted name: enoyl-CoA hydratase 2
Reaction: (3R)-3-hydroxyacyl-CoA = (2E)-2-enoyl-CoA + H2O
Other name(s): 2-enoyl-CoA hydratase 2; AtECH2; ECH2; MaoC; MFE-2; PhaJAc; D-3-hydroxyacyl-CoA hydro-lyase; D-specific 2-trans-enoyl-CoA hydratase
Systematic name: (3R)-3-hydroxyacyl-CoA hydro-lyase
Comments: This enzyme catalyses a hydration step in peroxisomal β-oxidation. The human multifunctional enzyme type 2 (MFE-2) is a 79000 Da enzyme composed of three functional units: (3R)-hydroxyacyl-CoA dehydrogenase, 2-enoyl-CoA hydratase 2 and sterol carrier protein 2-like units [1]. The enzymes from Aeromonas caviae [4] and Arabidopsis thaliana [5] are monofunctional enzymes. 2-Enoyl-CoA hydratase 3 from Candida tropicalis is a part from multifunctional enzyme type 2 [3].
References:
1.  Koski, K.M., Haapalainen, A.M., Hiltunen, J.K. and Glumoff, T. Crystal structure of 2-enoyl-CoA hydratase 2 from human peroxisomal multifunctional enzyme type 2. J. Mol. Biol. 345 (2005) 1157–1169. [PMID: 15644212]
2.  Fukui, T., Shiomi, N. and Doi, Y. Expression and characterization of (R)-specific enoyl coenzyme A hydratase involved in polyhydroxyalkanoate biosynthesis by Aeromonas caviae. J. Bacteriol. 180 (1998) 667–673. [PMID: 9457873]
3.  Koski, M.K., Haapalainen, A.M., Hiltunen, J.K. and Glumoff, T. Crystallization and preliminary crystallographic data of 2-enoyl-CoA hydratase 2 domain of Candida tropicalis peroxisomal multifunctional enzyme type 2. Acta Crystallogr. D Biol. Crystallogr. 59 (2003) 1302–1305. [PMID: 12832794]
4.  Hisano, T., Fukui, T., Iwata, T. and Doi, Y. Crystallization and preliminary X-ray analysis of (R)-specific enoyl-CoA hydratase from Aeromonas caviae involved in polyhydroxyalkanoate biosynthesis. Acta Crystallogr. D Biol. Crystallogr. 57 (2001) 145–147. [PMID: 11134939]
5.  Goepfert, S., Hiltunen, J.K. and Poirier, Y. Identification and functional characterization of a monofunctional peroxisomal enoyl-CoA hydratase 2 that participates in the degradation of even cis-unsaturated fatty acids in Arabidopsis thaliana. J. Biol. Chem. 281 (2006) 35894–35903. [PMID: 16982622]
6.  Engeland, K. and Kindl, H. Evidence for a peroxisomal fatty acid β-oxidation involving D-3-hydroxyacyl-CoAs. Characterization of two forms of hydro-lyase that convert D-(-)-3-hydroxyacyl-CoA into 2-trans-enoyl-CoA. Eur. J. Biochem. 200 (1991) 171–178. [PMID: 1879422]
[EC 4.2.1.119 created 2009]
 
 
EC 4.2.1.120     
Accepted name: 4-hydroxybutanoyl-CoA dehydratase
Reaction: 4-hydroxybutanoyl-CoA = (E)-but-2-enoyl-CoA + H2O
Glossary: 4-hydroxybutanoyl-CoA = 4-hydroxybutyryl-CoA
(E)-but-2-enoyl-CoA = crotonyl-CoA
Systematic name: 4-hydroxybutanoyl-CoA hydro-lyase
Comments: Contains FAD and a [4Fe-4S] iron-sulfur cluster. The enzyme has been characterized from several microorganisms, including Clostridium kluyveri, where it participates in succinate fermentation [1,2], Clostridium aminobutyricum, where it participates in 4-aminobutyrate degradation [3,4], and Metallosphaera sedula, where it participates in the 3-hydroxypropionate/4-hydroxybutyrate cycle, an autotrophic CO2 fixation pathway found in some thermoacidophilic archaea [5].
References:
1.  Bartsch, R.G. and Barker, H.A. A vinylacetyl isomerase from Clostridium kluyveri. Arch. Biochem. Biophys. 92 (1961) 122–132. [PMID: 13687513]
2.  Scherf, U., Sohling, B., Gottschalk, G., Linder, D. and Buckel, W. Succinate-ethanol fermentation in Clostridium kluyveri: purification and characterisation of 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA Δ32-isomerase. Arch. Microbiol. 161 (1994) 239–245. [PMID: 8161284]
3.  Scherf, U. and Buckel, W. Purification and properties of an iron-sulfur and FAD-containing 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA Δ32-isomerase from Clostridium aminobutyricum. Eur. J. Biochem. 215 (1993) 421–429. [PMID: 8344309]
4.  Muh, U., Cinkaya, I., Albracht, S.P. and Buckel, W. 4-Hydroxybutyryl-CoA dehydratase from Clostridium aminobutyricum: characterization of FAD and iron-sulfur clusters involved in an overall non-redox reaction. Biochemistry 35 (1996) 11710–11718. [PMID: 8794752]
5.  Berg, I.A., Kockelkorn, D., Buckel, W. and Fuchs, G. A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea. Science 318 (2007) 1782–1786. [PMID: 18079405]
[EC 4.2.1.120 created 2009]
 
 
EC 4.2.1.121     
Accepted name: colneleate synthase
Reaction: (9S,10E,12Z)-9-hydroperoxyoctadeca-10,12-dienoate = (8E)-9-[(1E,3Z)-nona-1,3-dien-1-yloxy]non-8-enoate + H2O
Glossary: colneleate = (8E)-9-[(1E,3Z)-nona-1,3-dien-1-yloxy]non-8-enoate
Other name(s): 9-divinyl ether synthase; 9-DES; CYP74D; CYP74D1; CYP74 cytochrome P-450; DES1; (8E)-9-[(1E,3E)-nona-1,3-dien-1-yloxy]non-8-enoate synthase
Systematic name: (9S,10E,12Z)-9-hydroperoxyoctadeca-10,12-dienoate hydro-lyase
Comments: A heme-thiolate protein (P-450) [2]. It catalyses the selective removal of pro-R hydrogen at C-8 in the biosynthesis of colneleic acid [4]. It forms also (8E)-9-[(1E,3Z,6Z)-nona-1,3,6-trien-1-yloxy]non-8-enoic acid (i.e. colnelenate) from (9S,10E,12Z,15Z)-9-hydroperoxy-10,12,15-octadecatrienoate. The corresponding 13-hydroperoxides are poor substrates [1,3]. The divinyl ethers colneleate and colnelenate have antimicrobial activity.
References:
1.  Stumpe, M., Kandzia, R., Gobel, C., Rosahl, S. and Feussner, I. A pathogen-inducible divinyl ether synthase (CYP74D) from elicitor-treated potato suspension cells. FEBS Lett. 507 (2001) 371–376. [PMID: 11696374]
2.  Itoh, A. and Howe, G.A. Molecular cloning of a divinyl ether synthase. Identification as a CYP74 cytochrome P-450. J. Biol. Chem. 276 (2001) 3620–3627. [PMID: 11060314]
3.  Fammartino, A., Cardinale, F., Gobel, C., Mene-Saffrane, L., Fournier, J., Feussner, I. and Esquerre-Tugaye, M.T. Characterization of a divinyl ether biosynthetic pathway specifically associated with pathogenesis in tobacco. Plant Physiol. 143 (2007) 378–388. [PMID: 17085514]
4.  Hamberg, M. Hidden stereospecificity in the biosynthesis of divinyl ether fatty acids. FEBS J. 272 (2005) 736–743. [PMID: 15670154]
[EC 4.2.1.121 created 2011, modified 2014]
 
 
EC 4.2.1.122     
Accepted name: tryptophan synthase (indole-salvaging)
Reaction: L-serine + indole = L-tryptophan + H2O
Other name(s): tryptophan synthase β2
Systematic name: L-serine hydro-lyase [adding indole, L-tryptophan-forming]
Comments: Most mesophilic bacteria have a multimeric tryptophan synthase complex (EC 4.2.1.20) that forms L-tryptophan from L-serine and 1-C-(indol-3-yl)glycerol 3-phosphate via an indole intermediate. This intermediate, which is formed by the α subunits, is transferred in an internal tunnel to the β units, which convert it to tryptophan. In thermophilic organisms the high temperature enhances diffusion and causes the loss of indole. This enzyme, which does not combine with the α unit to form a complex, salvages the lost indole back to L-tryptophan. It has a much lower Km for indole than the β subunit of EC 4.2.1.20.
References:
1.  Hettwer, S. and Sterner, R. A novel tryptophan synthase β-subunit from the hyperthermophile Thermotoga maritima. Quaternary structure, steady-state kinetics, and putative physiological role. J. Biol. Chem. 277 (2002) 8194–8201. [PMID: 11756459]
[EC 4.2.1.122 created 2011]
 
 
EC 4.2.1.123     
Accepted name: tetrahymanol synthase
Reaction: tetrahymanol = squalene + H2O
Glossary: tetrahymanol = gammaceran-3β-ol
Other name(s): squalene—tetrahymanol cyclase
Systematic name: squalene hydro-lyase (tetrahymanol forming)
Comments: The reaction occurs in the reverse direction.
References:
1.  Saar, J., Kader, J.C., Poralla, K. and Ourisson, G. Purification and some properties of the squalene-tetrahymanol cyclase from Tetrahymena thermophila. Biochim. Biophys. Acta 1075 (1991) 93–101. [PMID: 1892870]
2.  Giner, J.L., Rocchetti, S., Neunlist, S., Rohmer, M. and Arigoni, D. Detection of 1,2-hydride shifts in the formation of euph-7-ene by the squalene-tetrahymanol cyclase of Tetrahymena pyriformis. Chem. Commun. (Camb.) (2005) 3089–3091. [PMID: 15959594]
[EC 4.2.1.123 created 2011]
 
 
EC 4.2.1.124     
Accepted name: arabidiol synthase
Reaction: arabidiol = (3S)-2,3-epoxy-2,3-dihydrosqualene + H2O
Glossary: arabidiol = (13R)-malabarica-17,21-diene-3β,14-diol
Other name(s): PEN1 (gene name); (S)-squalene-2,3-epoxide hydro-lyase (arabidiol forming)
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene hydro-lyase (arabidiol forming)
Comments: The reaction occurs in the reverse direction.
References:
1.  Xiang, T., Shibuya, M., Katsube, Y., Tsutsumi, T., Otsuka, M., Zhang, H., Masuda, K. and Ebizuka, Y. A new triterpene synthase from Arabidopsis thaliana produces a tricyclic triterpene with two hydroxyl groups. Org. Lett. 8 (2006) 2835–2838. [PMID: 16774269]
[EC 4.2.1.124 created 2011]
 
 
EC 4.2.1.125     
Accepted name: dammarenediol II synthase
Reaction: dammarenediol II = (3S)-2,3-epoxy-2,3-dihydrosqualene + H2O
Other name(s): dammarenediol synthase; 2,3-oxidosqualene (20S)-dammarenediol cyclase; DDS; (S)-squalene-2,3-epoxide hydro-lyase (dammarenediol-II forming)
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene hydro-lyase (dammarenediol-II forming)
Comments: The reaction occurs in the reverse direction.
References:
1.  Tansakul, P., Shibuya, M., Kushiro, T. and Ebizuka, Y. Dammarenediol-II synthase, the first dedicated enzyme for ginsenoside biosynthesis, in Panax ginseng. FEBS Lett. 580 (2006) 5143–5149. [PMID: 16962103]
2.  Han, J.Y., Kwon, Y.S., Yang, D.C., Jung, Y.R. and Choi, Y.E. Expression and RNA interference-induced silencing of the dammarenediol synthase gene in Panax ginseng. Plant Cell Physiol. 47 (2006) 1653–1662. [PMID: 17088293]
[EC 4.2.1.125 created 2011]
 
 
EC 4.2.1.126     
Accepted name: N-acetylmuramic acid 6-phosphate etherase
Reaction: (R)-lactate + N-acetyl-D-glucosamine 6-phosphate = N-acetylmuramate 6-phosphate + H2O
Other name(s): MurNAc-6-P etherase; MurQ
Systematic name: (R)-lactate hydro-lyase (adding N-acetyl-D-glucosamine 6-phosphate; N-acetylmuramate 6-phosphate-forming)
Comments: This enzyme, along with EC 2.7.1.170, anhydro-N-acetylmuramic acid kinase, is required for the utilization of anhydro-N-acetylmuramic acid in proteobacteria. The substrate is either imported from the medium or derived from the bacterium’s own cell wall murein during cell wall recycling.
References:
1.  Jaeger, T., Arsic, M. and Mayer, C. Scission of the lactyl ether bond of N-acetylmuramic acid by Escherichia coli "etherase". J. Biol. Chem. 280 (2005) 30100–30106. [PMID: 15983044]
2.  Uehara, T., Suefuji, K., Valbuena, N., Meehan, B., Donegan, M. and Park, J.T. Recycling of the anhydro-N-acetylmuramic acid derived from cell wall murein involves a two-step conversion to N-acetylglucosamine-phosphate. J. Bacteriol. 187 (2005) 3643–3649. [PMID: 15901686]
3.  Uehara, T., Suefuji, K., Jaeger, T., Mayer, C. and Park, J.T. MurQ etherase is required by Escherichia coli in order to metabolize anhydro-N-acetylmuramic acid obtained either from the environment or from its own cell wall. J. Bacteriol. 188 (2006) 1660–1662. [PMID: 16452451]
4.  Hadi, T., Dahl, U., Mayer, C. and Tanner, M.E. Mechanistic studies on N-acetylmuramic acid 6-phosphate hydrolase (MurQ): an etherase involved in peptidoglycan recycling. Biochemistry 47 (2008) 11547–11558. [PMID: 18837509]
5.  Jaeger, T. and Mayer, C. N-acetylmuramic acid 6-phosphate lyases (MurNAc etherases): role in cell wall metabolism, distribution, structure, and mechanism. Cell. Mol. Life Sci. 65 (2008) 928–939. [PMID: 18049859]
[EC 4.2.1.126 created 2011]
 
 
EC 4.2.1.127     
Accepted name: linalool dehydratase
Reaction: (3S)-linalool = myrcene + H2O
Glossary: linalool = 3,7-dimethylocta-1,6-dien-3-ol
Other name(s): linalool hydro-lyase (myrcene-forming)
Systematic name: (3S)-linalool hydro-lyase (myrcene-forming)
Comments: In absence of oxygen the bifunctional linalool dehydratase-isomerase can catalyse in vitro two reactions, the hydration of myrcene to (3S)-linalool and the isomerization of (3S)-linalool to geraniol, the latter activity being classified as EC 5.4.4.4, geraniol isomerase.
References:
1.  Brodkorb, D., Gottschall, M., Marmulla, R., Lüddeke, F. and Harder, J. Linalool dehydratase-isomerase, a bifunctional enzyme in the anaerobic degradation of monoterpenes. J. Biol. Chem. 285 (2010) 30436–30442. [PMID: 20663876]
2.  Lüddeke, F. and Harder, J. Enantiospecific (S)-(+)-linalool formation from β-myrcene by linalool dehydratase-isomerase. Z. Naturforsch. C 66 (2011) 409–412. [PMID: 21950166]
[EC 4.2.1.127 created 2011, modified 2012]
 
 
EC 4.2.1.128     
Accepted name: lupan-3β,20-diol synthase
Reaction: lupan-3β,20-diol = (3S)-2,3-epoxy-2,3-dihydrosqualene + H2O
Other name(s): LUP1 (gene name)
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene hydro-lyase (lupan-3β,20-diol forming)
Comments: The reaction occurs in the reverse direction. The recombinant enzyme from Arabidopsis thaliana gives a 1:1 mixture of lupeol and lupan-3β,20-diol with small amounts of β-amyrin, germanicol, taraxasterol and ψ-taraxasterol. See EC 5.4.99.41 (lupeol synthase).
References:
1.  Segura, M.J., Meyer, M.M. and Matsuda, S.P. Arabidopsis thaliana LUP1 converts oxidosqualene to multiple triterpene alcohols and a triterpene diol. Org. Lett. 2 (2000) 2257–2259. [PMID: 10930257]
2.  Kushiro, T., Hoshino, M., Tsutsumi, T., Kawai, K., Shiro, M., Shibuya, M. and Ebizuka, Y. Stereochemical course in water addition during LUP1-catalyzed triterpene cyclization. Org. Lett. 8 (2006) 5589–5592. [PMID: 17107079]
[EC 4.2.1.128 created 2011]
 
 
EC 4.2.1.129     
Accepted name: squalene—hopanol cyclase
Reaction: hopan-22-ol = squalene + H2O
Other name(s): squalene—hopene cyclase (ambiguous)
Systematic name: hopan-22-ol hydro-lyase
Comments: The enzyme produces the cyclization products hopene (cf. EC 5.4.99.17) and hopanol from squalene at a constant ratio of 5:1.
References:
1.  Hoshino, T., Nakano, S., Kondo, T., Sato, T. and Miyoshi, A. Squalene-hopene cyclase: final deprotonation reaction, conformational analysis for the cyclization of (3R,S)-2,3-oxidosqualene and further evidence for the requirement of an isopropylidene moiety both for initiation of the polycyclization cascade and for the formation of the 5-membered E-ring. Org Biomol Chem 2 (2004) 1456–1470. [PMID: 15136801]
2.  Sato, T., Kouda, M. and Hoshino, T. Site-directed mutagenesis experiments on the putative deprotonation site of squalene-hopene cyclase from Alicyclobacillus acidocaldarius. Biosci. Biotechnol. Biochem. 68 (2004) 728–738. [PMID: 15056909]
[EC 4.2.1.129 created 2011]
 
 
EC 4.2.1.130     
Accepted name: D-lactate dehydratase
Reaction: (R)-lactate = 2-oxopropanal + H2O
Glossary: methylglyoxal = 2-oxopropanal
(R)-lactate = D-lactate
Other name(s): glyoxylase III; GLO3
Systematic name: (R)-lactate hydro-lyase
Comments: The enzyme, described from the fungi Candida albicans and Schizosaccharomyces pombe, converts 2-oxopropanal to (R)-lactate in a single glutathione (GSH)-independent step. The other known route for this conversion is the two-step GSH-dependent pathway catalysed by EC 4.4.1.5 (lactoylglutathione lyase) and EC 3.1.2.6 (hydroxyacylglutathione hydrolase).
References:
1.  Hasim, S., Hussin, N.A., Alomar, F., Bidasee, K.R., Nickerson, K.W. and Wilson, M.A. A glutathione-independent glyoxalase of the DJ-1 superfamily plays an important role in managing metabolically generated methylglyoxal in Candida albicans. J. Biol. Chem. 289 (2014) 1662–1674. [PMID: 24302734]
2.  Zhao, Q., Su, Y., Wang, Z., Chen, C., Wu, T. and Huang, Y. Identification of glutathione (GSH)-independent glyoxalase III from Schizosaccharomyces pombe. BMC Evol Biol 14:86 (2014). [PMID: 24758716]
[EC 4.2.1.130 created 2011]
 
 
EC 4.2.1.131     
Accepted name: carotenoid 1,2-hydratase
Reaction: (1) 1-hydroxy-1,2-dihydrolycopene = lycopene + H2O
(2) 1,1′-dihydroxy-1,1′,2,2′-tetrahydrolycopene = 1-hydroxy-1,2-dihydrolycopene + H2O
Other name(s): CrtC
Systematic name: lycopene hydro-lyase (1-hydroxy-1,2-dihydrolycopene-forming)
Comments: In Rubrivivax gelatinosus [1] and Thiocapsa roseopersicina [2] both products are formed, whereas Rhodobacter capsulatus [1] only gives 1-hydroxy-1,2-dihydrolycopene. Also acts on neurosporene giving 1-hydroxy-1,2-dihydroneurosporene with both organism but 1,1′-dihydroxy-1,1′,2,2′-tetrahydroneurosporene only with Rubrivivax gelatinosus.
References:
1.  Steiger, S., Mazet, A. and Sandmann, G. Heterologous expression, purification, and enzymatic characterization of the acyclic carotenoid 1,2-hydratase from Rubrivivax gelatinosus. Arch. Biochem. Biophys. 414 (2003) 51–58. [PMID: 12745254]
2.  Hiseni, A., Arends, I.W. and Otten, L.G. Biochemical characterization of the carotenoid 1,2-hydratases (CrtC) from Rubrivivax gelatinosus and Thiocapsa roseopersicina. Appl. Microbiol. Biotechnol. 91 (2011) 1029–1036. [PMID: 21590288]
[EC 4.2.1.131 created 2011]
 
 
EC 4.2.1.132     
Accepted name: 2-hydroxyhexa-2,4-dienoate hydratase
Reaction: 4-hydroxy-2-oxohexanoate = (2Z,4Z)-2-hydroxyhexa-2,4-dienoate + H2O
Other name(s): tesE (gene name); hsaE (gene name)
Systematic name: 4-hydroxy-2-oxohexanoate hydro-lyase [(2Z,4Z)-2-hydroxyhexa-2,4-dienoate-forming]
Comments: This enzyme catalyses a late step in the bacterial steroid degradation pathway. The product, 4-hydroxy-2-oxohexanoate, forms a 2-hydroxy-4-hex-2-enolactone under acidic conditions.
References:
1.  Horinouchi, M., Hayashi, T., Koshino, H., Kurita, T. and Kudo, T. Identification of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid, 4-hydroxy-2-oxohexanoic acid, and 2-hydroxyhexa-2,4-dienoic acid and related enzymes involved in testosterone degradation in Comamonas testosteroni TA441. Appl. Environ. Microbiol. 71 (2005) 5275–5281. [PMID: 16151114]
[EC 4.2.1.132 created 2012]
 
 
EC 4.2.1.133     
Accepted name: copal-8-ol diphosphate hydratase
Reaction: (13E)-8α-hydroxylabd-13-en-15-yl diphosphate = geranylgeranyl diphosphate + H2O
Glossary: (13E)-8α-hydroxylabd-13-en-15-yl diphosphate = 8-hydroxycopalyl diphosphate
Other name(s): CcCLS
Systematic name: geranylgeranyl-diphosphate hydro-lyase [(13E)-8α-hydroxylabd-13-en-15-yl diphosphate forming]
Comments: Requires Mg2+. The enzyme was characterized from the plant Cistus creticus subsp. creticus.
References:
1.  Falara, V., Pichersky, E. and Kanellis, A.K. A copal-8-ol diphosphate synthase from the angiosperm Cistus creticus subsp. creticus is a putative key enzyme for the formation of pharmacologically active, oxygen-containing labdane-type diterpenes. Plant Physiol. 154 (2010) 301–310. [PMID: 20595348]
[EC 4.2.1.133 created 2012]
 
 
EC 4.2.1.134     
Accepted name: very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase
Reaction: a very-long-chain (3R)-3-hydroxyacyl-CoA = a very-long-chain trans-2,3-dehydroacyl-CoA + H2O
Glossary: a very-long-chain acyl-CoA = an acyl-CoA thioester where the acyl chain contains 23 or more carbon atoms.
Other name(s): PHS1 (gene name); PAS2 (gene name)
Systematic name: very-long-chain (3R)-3-hydroxyacyl-CoA hydro-lyase
Comments: This is the third component of the elongase, a microsomal protein complex responsible for extending palmitoyl-CoA and stearoyl-CoA (and modified forms thereof) to very-long chain acyl CoAs. cf. EC 2.3.1.199, very-long-chain 3-oxoacyl-CoA synthase, EC 1.1.1.330, very-long-chain 3-oxoacyl-CoA reductase, and EC 1.3.1.93, very-long-chain enoyl-CoA reductase.
References:
1.  Bach, L., Michaelson, L.V., Haslam, R., Bellec, Y., Gissot, L., Marion, J., Da Costa, M., Boutin, J.P., Miquel, M., Tellier, F., Domergue, F., Markham, J.E., Beaudoin, F., Napier, J.A. and Faure, J.D. The very-long-chain hydroxy fatty acyl-CoA dehydratase PASTICCINO2 is essential and limiting for plant development. Proc. Natl. Acad. Sci. USA 105 (2008) 14727–14731. [PMID: 18799749]
2.  Kihara, A., Sakuraba, H., Ikeda, M., Denpoh, A. and Igarashi, Y. Membrane topology and essential amino acid residues of Phs1, a 3-hydroxyacyl-CoA dehydratase involved in very long-chain fatty acid elongation. J. Biol. Chem. 283 (2008) 11199–11209. [PMID: 18272525]
[EC 4.2.1.134 created 2012, modified 2014]
 
 
EC 4.2.1.135     
Accepted name: UDP-N-acetylglucosamine 4,6-dehydratase (configuration-retaining)
Reaction: UDP-N-acetyl-α-D-glucosamine = UDP-2-acetamido-2,6-dideoxy-α-D-xylo-hex-4-ulose + H2O
Glossary: N,N′-diacetylbacillosamine = 2,4-diacetamido-2,4,6-trideoxy-α-D-glucopyranose
Other name(s): PglF
Systematic name: UDP-N-acetyl-α-D-glucosamine hydro-lyase (configuration-retaining; UDP-2-acetamido-2,6-dideoxy-α-D-xylo-hex-4-ulose-forming)
Comments: Contains NAD+ as a cofactor [2]. This is the first enzyme in the biosynthetic pathway of N,N′-diacetylbacillosamine [1], the first carbohydrate in the glycoprotein N-linked heptasaccharide in Campylobacter jejuni. This enzyme belongs to the short-chain dehydrogenase/reductase family of enzymes.
References:
1.  Schoenhofen, I.C., McNally, D.J., Vinogradov, E., Whitfield, D., Young, N.M., Dick, S., Wakarchuk, W.W., Brisson, J.R. and Logan, S.M. Functional characterization of dehydratase/aminotransferase pairs from Helicobacter and Campylobacter: enzymes distinguishing the pseudaminic acid and bacillosamine biosynthetic pathways. J. Biol. Chem. 281 (2006) 723–732. [PMID: 16286454]
2.  Olivier, N.B., Chen, M.M., Behr, J.R. and Imperiali, B. In vitro biosynthesis of UDP-N,N′-diacetylbacillosamine by enzymes of the Campylobacter jejuni general protein glycosylation system. Biochemistry 45 (2006) 13659–13669. [PMID: 17087520]
[EC 4.2.1.135 created 2012]
 
 
EC 4.2.1.136     
Accepted name: ADP-dependent NAD(P)H-hydrate dehydratase
Reaction: (1) ADP + (6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide = AMP + phosphate + NADH
(2) ADP + (6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide phosphate = AMP + phosphate + NADPH
Glossary: (6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide = (S)-NADH-hydrate = (S)-NADHX
(6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide phosphate = (S)-NADPH-hydrate = (S)-NADPHX
Other name(s): (6S)-β-6-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine-dinucleotide hydro-lyase(ADP-hydrolysing); (6S)-6-β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine-dinucleotide hydro-lyase (ADP-hydrolysing; NADH-forming)
Systematic name: (6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine-dinucleotide hydro-lyase (ADP-hydrolysing; NADH-forming)
Comments: Acts equally well on hydrated NADH and hydrated NADPH. NAD(P)H spontaneously hydrates to both the (6S)- and (6R)- isomers. The enzyme from bacteria consists of two domains, one of which acts as an NAD(P)H-hydrate epimerase that interconverts the two isomers to a 60:40 ratio (cf. EC 5.1.99.6), while the other catalyses the dehydration. Hence the enzyme can restore the complete mixture of isomers into NAD(P)H. The enzyme has no activity with ATP, contrary to the enzyme from eukaryotes (cf. EC 4.2.1.93, ATP-dependent NAD(P)H-hydrate dehydratase).
References:
1.  Marbaix, A.Y., Noel, G., Detroux, A.M., Vertommen, D., Van Schaftingen, E. and Linster, C.L. Extremely conserved ATP- or ADP-dependent enzymatic system for nicotinamide nucleotide repair. J. Biol. Chem. 286 (2011) 41246–41252. [PMID: 21994945]
[EC 4.2.1.136 created 2012]
 
 
EC 4.2.1.137     
Accepted name: sporulenol synthase
Reaction: sporulenol = tetraprenyl-β-curcumene + H2O
Glossary: sporulenol = (1R,2R,4aS,4bR,6aS,10aS,10bR,12aS)-2,4b,7,7,10a,12a-hexamethyl-1-[(3R)-3-(4-methylcyclohexa-1,4-dien-1-yl)butyl]octadecahydrochrysen-2-ol
Other name(s): sqhC (gene name)
Systematic name: tetraprenyl-β-curcumene—sporulenol cyclase
Comments: The reaction occurs in the reverse direction. Isolated from Bacillus subtilis. Similar sesquarterpenoids are present in a number of Bacillus species.
References:
1.  Sato, T., Yoshida, S., Hoshino, H., Tanno, M., Nakajima, M. and Hoshino, T. Sesquarterpenes (C35 terpenes) biosynthesized via the cyclization of a linear C35 isoprenoid by a tetraprenyl-β-curcumene synthase and a tetraprenyl-β-curcumene cyclase: identification of a new terpene cyclase. J. Am. Chem. Soc. 133 (2011) 9734–9737. [PMID: 21627333]
[EC 4.2.1.137 created 2012]
 
 
EC 4.2.1.138     
Accepted name: (+)-caryolan-1-ol synthase
Reaction: (+)-β-caryophyllene + H2O = (+)-caryolan-1-ol
Glossary: (+)-caryolan-1-ol = (1S,2R,5S,8R)-4,4,8-trimethyltricyclo[6.3.1.02,5]dodecan-1-ol
Other name(s): GcoA
Systematic name: (+)-β-caryophyllene hydrolase [cyclizing, (+)-caryolan-1-ol-forming]
Comments: A multifunctional enzyme which also forms (+)-β-caryophyllene from farnesyl diphosphate [EC 4.2.3.89, (+)-β-caryophyllene synthase].
References:
1.  Nakano, C., Horinouchi, S. and Ohnishi, Y. Characterization of a novel sesquiterpene cyclase involved in (+)-caryolan-1-ol biosynthesis in Streptomyces griseus. J. Biol. Chem. 286 (2011) 27980–27987. [PMID: 21693706]
[EC 4.2.1.138 created 2011 as EC 3.7.1.15, transferred 2013 to EC 4.2.1.138]
 
 
EC 4.2.1.139     
Accepted name: pterocarpan synthase
Reaction: a (4R)-4,2′-dihydroxyisoflavan = a pterocarpan + H2O
Glossary: an isoflavan = an isoflavonoid with a 3,4-dihydro-3-aryl-2H-1-benzopyran skeleton.
(–)-medicarpin = (6aR,11aR)-9-methoxy-6a,11a-dihydro-6H-[1]benzofuro[3,2-c]chromen-3-ol
(+)-medicarpin = (6aS,11aS)-9-methoxy-6a,11a-dihydro-6H-[1]benzofuro[3,2-c]chromen-3-ol
(–)-maackiain = (6aR,12aR)-6a,12a-dihydro-6H-[1,3]dioxolo[5,6][1]benzofuro[3,2-c]chromen-3-ol
(+)-maackiain = (6aS,12aS)-6a,12a-dihydro-6H-[1,3]dioxolo[5,6][1]benzofuro[3,2-c]chromen-3-ol
(+)-pterocarpan = (6aR,11aR)-6a,11a-dihydro-6H-[1]benzofuran[3,2-c][1]benzopyran
Other name(s): medicarpin synthase; medicarpan synthase; 7,2′-dihydroxy-4′-methoxyisoflavanol dehydratase; 2′,7-dihydroxy-4′-methoxyisoflavanol dehydratase; DMI dehydratase; DMID; 2′-hydroxyisoflavanol 4,2′-dehydratase; PTS (gene name); 4′-methoxyisoflavan-2′,4,7-triol hydro-lyase [(–)-medicarpin-forming]
Systematic name: (4R)-4,2′-dihydroxyisoflavan hydro-lyase (pterocarpan-forming)
Comments: The enzyme catalyses the formation of the additional ring in pterocarpan, the basic structure of phytoalexins produced by leguminous plants, including (–)-medicarpin, (+)-medicarpin, (–)-maackiain and (+)-maackiain. The enzyme requires that the hydroxyl group at C-4 of the substrate is in the (4R) configuration. The configuration of the hydrogen atom at C-3 determines whether the pterocarpan is the (+)- or (–)-enantiomer. The enzyme contains amino acid motifs characteristic of dirigent proteins.
References:
1.  Guo, L., Dixon, R.A. and Paiva, N.L. The ‘pterocarpan synthase’ of alfalfa: association and co-induction of vestitone reductase and 7,2′-dihydroxy-4′-methoxy-isoflavanol (DMI) dehydratase, the two final enzymes in medicarpin biosynthesis. FEBS Lett. 356 (1994) 221–225. [PMID: 7805842]
2.  Guo, L., Dixon, R.A. and Paiva, N.L. Conversion of vestitone to medicarpin in alfalfa (Medicago sativa L.) is catalyzed by two independent enzymes. Identification, purification, and characterization of vestitone reductase and 7,2′-dihydroxy-4′-methoxyisoflavanol dehydratase. J. Biol. Chem. 269 (1994) 22372–22378. [PMID: 8071365]
3.  Uchida, K., Akashi, T. and Aoki, T. The missing link in leguminous pterocarpan biosynthesis is a dirigent domain-containing protein with isoflavanol dehydratase activity. Plant Cell Physiol. 58 (2017) 398–408. [PMID: 28394400]
[EC 4.2.1.139 created 2013, modified 2019]
 
 
EC 4.2.1.140     
Accepted name: gluconate/galactonate dehydratase
Reaction: (1) D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O
(2) D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O
Other name(s): gluconate dehydratase (ambiguous); Sso3198 (gene name); Pto0485 (gene name)
Systematic name: D-gluconate/D-galactonate hydro-lyase
Comments: The enzyme is involved in glucose and galactose catabolism via the nonphosphorylative variant of the Entner-Doudoroff pathway in Picrophilus torridus [3] and via the branched variant of the Entner-Doudoroff pathway in Sulfolobus solfataricus [1,2]. In vitro it utilizes D-gluconate with 6-10 fold higher catalytic efficiency than D-galactonate [1,3]. It requires Mg2+ for activity [1,2]. cf. EC 4.2.1.6, galactonate dehydratase, and EC 4.2.1.39, gluconate dehydratase.
References:
1.  Lamble, H.J., Milburn, C.C., Taylor, G.L., Hough, D.W. and Danson, M.J. Gluconate dehydratase from the promiscuous Entner-Doudoroff pathway in Sulfolobus solfataricus. FEBS Lett. 576 (2004) 133–136. [PMID: 15474024]
2.  Ahmed, H., Ettema, T.J., Tjaden, B., Geerling, A.C., van der Oost, J. and Siebers, B. The semi-phosphorylative Entner-Doudoroff pathway in hyperthermophilic archaea: a re-evaluation. Biochem. J. 390 (2005) 529–540. [PMID: 15869466]
3.  Reher, M., Fuhrer, T., Bott, M. and Schonheit, P. The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate- specific aldolase. J. Bacteriol. 192 (2010) 964–974. [PMID: 20023024]
[EC 4.2.1.140 created 2013]
 
 
EC 4.2.1.141     
Accepted name: 2-dehydro-3-deoxy-D-arabinonate dehydratase
Reaction: 2-dehydro-3-deoxy-D-arabinonate = 2,5-dioxopentanoate + H2O
Glossary: 2-dehydro-3-deoxy-D-arabinonate = 2-dehydro-3-deoxy-D-xylonate = 3-deoxy-L-glycero-pent-2-ulonate
Systematic name: 2-dehydro-3-deoxy-D-arabinonate hydro-lyase (2,5-dioxopentanoate-forming)
Comments: The enzyme participates in pentose oxidation pathways that convert pentose sugars to the tricarboxylic acid cycle intermediate 2-oxoglutarate.
References:
1.  Brouns, S.J., Walther, J., Snijders, A.P., van de Werken, H.J., Willemen, H.L., Worm, P., de Vos, M.G., Andersson, A., Lundgren, M., Mazon, H.F., van den Heuvel, R.H., Nilsson, P., Salmon, L., de Vos, W.M., Wright, P.C., Bernander, R. and van der Oost, J. Identification of the missing links in prokaryotic pentose oxidation pathways: evidence for enzyme recruitment. J. Biol. Chem. 281 (2006) 27378–27388. [PMID: 16849334]
2.  Brouns, S.J., Barends, T.R., Worm, P., Akerboom, J., Turnbull, A.P., Salmon, L. and van der Oost, J. Structural insight into substrate binding and catalysis of a novel 2-keto-3-deoxy-D-arabinonate dehydratase illustrates common mechanistic features of the FAH superfamily. J. Mol. Biol. 379 (2008) 357–371. [PMID: 18448118]
3.  Johnsen, U., Dambeck, M., Zaiss, H., Fuhrer, T., Soppa, J., Sauer, U. and Schonheit, P. D-Xylose degradation pathway in the halophilic archaeon Haloferax volcanii. J. Biol. Chem. 284 (2009) 27290–27303. [PMID: 19584053]
[EC 4.2.1.141 created 2013]
 
 
EC 4.2.1.142     
Accepted name: 5′-oxoaverantin cyclase
Reaction: 5′-oxoaverantin = (1′S,5′S)-averufin + H2O
Glossary: 5′-oxoaverantin = 1,3,6,8-tetrahydroxy-2-[(1S)-1-hydroxy-5-oxohexyl]anthracene-9,10-dione
averufin = 7,9,11-trihydroxy-2-methyl-3,4,5,6-tetrahydro-2,6-epoxy-2H-anthra[2,3-b]oxocin-8,13-dione
Other name(s): OAVN cyclase; 5′-oxoaverantin hydro-lyase [(2′S,5′S)-averufin forming]
Systematic name: 5′-oxoaverantin hydro-lyase [(1′S,5′S)-averufin forming]
Comments: Isolated from the aflatoxin-producing mold Aspergillus parasiticus. The enzyme also catalyses the conversion of versiconal to versicolorin B (EC 4.2.1.143, versicolorin B synthase). Involved in aflatoxin biosynthesis.
References:
1.  Sakuno, E., Yabe, K. and Nakajima, H. Involvement of two cytosolic enzymes and a novel intermediate, 5′-oxoaverantin, in the pathway from 5′-hydroxyaverantin to averufin in aflatoxin biosynthesis. Appl. Environ. Microbiol. 69 (2003) 6418–6426. [PMID: 14602595]
2.  Sakuno, E., Wen, Y., Hatabayashi, H., Arai, H., Aoki, C., Yabe, K. and Nakajima, H. Aspergillus parasiticus cyclase catalyzes two dehydration steps in aflatoxin biosynthesis. Appl. Environ. Microbiol. 71 (2005) 2999–3006. [PMID: 15932995]
[EC 4.2.1.142 created 2013]
 
 
EC 4.2.1.143     
Accepted name: versicolorin B synthase
Reaction: versiconal = versicolorin B + H2O
Glossary: versiconal = (2S,3S)-2,4,6,8-tetrahydroxy-3-(2-hydroxyethyl)anthra[2,3-b]furan-5,10-dione
versicolorin B = (3aR,12bS)-8,10,12-trihydroxy-1,2,3a,12b-tetrahydroanthra[2,3-b]furo[3,2-d]furan-6,11-dione
Other name(s): versiconal cyclase; VBS
Systematic name: versiconal hydro-lyase (versicolorin-B forming)
Comments: Isolated from the aflatoxin-producing mold Aspergillus parasiticus. Involved in aflatoxin biosynthesis.
References:
1.  Lin, B.K. and Anderson, J.A. Purification and properties of versiconal cyclase from Aspergillus parasiticus. Arch. Biochem. Biophys. 293 (1992) 67–70. [PMID: 1731640]
2.  McGuire, S.M., Silva, J.C., Casillas, E.G. and Townsend, C.A. Purification and characterization of versicolorin B synthase from Aspergillus parasiticus. Catalysis of the stereodifferentiating cyclization in aflatoxin biosynthesis essential to DNA interaction. Biochemistry 35 (1996) 11470–11486. [PMID: 8784203]
3.  Silva, J.C., Minto, R.E., Barry, C.E., 3rd, Holland, K.A. and Townsend, C.A. Isolation and characterization of the versicolorin B synthase gene from Aspergillus parasiticus. Expansion of the aflatoxin b1 biosynthetic gene cluster. J. Biol. Chem. 271 (1996) 13600–13608. [PMID: 8662689]
4.  Silva, J.C. and Townsend, C.A. Heterologous expression, isolation, and characterization of versicolorin B synthase from Aspergillus parasiticus. A key enzyme in the aflatoxin B1 biosynthetic pathway. J. Biol. Chem. 272 (1997) 804–813. [PMID: 8995367]
[EC 4.2.1.143 created 2013]
 
 
EC 4.2.1.144     
Accepted name: 3-amino-5-hydroxybenzoate synthase
Reaction: 5-amino-5-deoxy-3-dehydroshikimate = 3-amino-5-hydroxybenzoate + H2O
Other name(s): AHBA synthase; rifK (gene name)
Systematic name: 5-amino-5-deoxy-3-dehydroshikimate hydro-lyase (3-amino-5-hydroxybenzoate-forming)
Comments: A pyridoxal 5′-phosphate enzyme. The enzyme from the bacterium Amycolatopsis mediterranei participates in the pathway for rifamycin B biosynthesis. The enzyme also functions as a transaminase earlier in the pathway, producing UDP-α-D-kanosamine [3].
References:
1.  Kim, C.G., Yu, T.W., Fryhle, C.B., Handa, S. and Floss, H.G. 3-Amino-5-hydroxybenzoic acid synthase, the terminal enzyme in the formation of the precursor of mC7N units in rifamycin and related antibiotics. J. Biol. Chem. 273 (1998) 6030–6040. [PMID: 9497318]
2.  Eads, J.C., Beeby, M., Scapin, G., Yu, T.W. and Floss, H.G. Crystal structure of 3-amino-5-hydroxybenzoic acid (AHBA) synthase. Biochemistry 38 (1999) 9840–9849. [PMID: 10433690]
3.  Floss, H.G., Yu, T.W. and Arakawa, K. The biosynthesis of 3-amino-5-hydroxybenzoic acid (AHBA), the precursor of mC7N units in ansamycin and mitomycin antibiotics: a review. J. Antibiot. (Tokyo) 64 (2011) 35–44. [PMID: 21081954]
[EC 4.2.1.144 created 2013]
 
 
EC 4.2.1.145     
Accepted name: capreomycidine synthase
Reaction: (2S,3S)-3-hydroxyarginine = (2S,3R)-capreomycidine + H2O
Glossary: (2S,3R)-capreomycidine = (S)-2-amino-2-[(R)-2-iminohexahydropyrimidin-4-yl]acetic acid
Other name(s): VioD (ambiguous)
Systematic name: (2S,3S)-3-hydroxyarginine hydro-lyase (cyclizing, (2S,3R)-capreomycidine-forming)
Comments: A pyridoxal 5′-phosphate protein. The enzyme is involved in the biosynthesis of the cyclic pentapeptide antibiotic viomycin.
References:
1.  Yin, X., McPhail, K.L., Kim, K.J. and Zabriskie, T.M. Formation of the nonproteinogenic amino acid (2S,3R)-capreomycidine by VioD from the viomycin biosynthesis pathway. ChemBioChem 5 (2004) 1278–1281. [PMID: 15368581]
2.  Ju, J., Ozanick, S.G., Shen, B. and Thomas, M.G. Conversion of (2S)-arginine to (2S,3R)-capreomycidine by VioC and VioD from the viomycin biosynthetic pathway of Streptomyces sp. strain ATCC11861. ChemBioChem 5 (2004) 1281–1285. [PMID: 15368582]
[EC 4.2.1.145 created 2013]
 
 
EC 4.2.1.146     
Accepted name: L-galactonate dehydratase
Reaction: L-galactonate = 2-dehydro-3-deoxy-L-galactonate + H2O
Other name(s): LGD1
Systematic name: L-galactonate hydro-lyase (2-dehydro-3-deoxy-L-galactonate-forming)
Comments: The enzyme takes part in a D-galacturonate degradation pathway in the fungi Trichoderma reesei (Hypocrea jecorina) and Aspergillus niger.
References:
1.  Kuorelahti, S., Jouhten, P., Maaheimo, H., Penttila, M. and Richard, P. L-Galactonate dehydratase is part of the fungal path for D-galacturonic acid catabolism. Mol. Microbiol. 61 (2006) 1060–1068. [PMID: 16879654]
2.  Martens-Uzunova, E.S. and Schaap, P.J. An evolutionary conserved D-galacturonic acid metabolic pathway operates across filamentous fungi capable of pectin degradation. Fungal Genet. Biol. 45 (2008) 1449–1457. [PMID: 18768163]
[EC 4.2.1.146 created 2013]
 
 
EC 4.2.1.147     
Accepted name: 5,6,7,8-tetrahydromethanopterin hydro-lyase
Reaction: 5,6,7,8-tetrahydromethanopterin + formaldehyde = 5,10-methylenetetrahydromethanopterin + H2O
Other name(s): formaldehyde-activating enzyme
Systematic name: 5,6,7,8-tetrahydromethanopterin hydro-lyase (formaldehyde-adding, tetrahydromethanopterin-forming)
Comments: Found in methylotrophic bacteria and methanogenic archaea.
References:
1.  Vorholt, J.A., Marx, C.J., Lidstrom, M.E. and Thauer, R.K. Novel formaldehyde-activating enzyme in Methylobacterium extorquens AM1 required for growth on methanol. J. Bacteriol. 182 (2000) 6645–6650. [PMID: 11073907]
2.  Acharya, P., Goenrich, M., Hagemeier, C.H., Demmer, U., Vorholt, J.A., Thauer, R.K. and Ermler, U. How an enzyme binds the C1 carrier tetrahydromethanopterin. Structure of the tetrahydromethanopterin-dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1. J. Biol. Chem. 280 (2005) 13712–13719. [PMID: 15632161]
[EC 4.2.1.147 created 2014]
 
 
EC 4.2.1.148     
Accepted name: 2-methylfumaryl-CoA hydratase
Reaction: (2R,3S)-2-methylmalyl-CoA = 2-methylfumaryl-CoA + H2O
Glossary: (2R,3S)-2-methylmalyl-CoA = L-erythro-β-methylmalyl-CoA = (2R,3S)-2-methyl-3-carboxy-3-hydroxypropanoyl-CoA
2-methylfumaryl-CoA = (E)-3-carboxy-2-methylprop-2-enoyl-CoA
Other name(s): Mcd; erythro-β-methylmalonyl-CoA hydrolyase; mesaconyl-coenzyme A hydratase (ambiguous); mesaconyl-C1-CoA hydratase
Systematic name: (2R,3S)-2-methylmalyl-CoA hydro-lyase (2-methylfumaryl-CoA-forming)
Comments: The enzyme from the bacterium Chloroflexus aurantiacus is part of the 3-hydroxypropanoate cycle for carbon assimilation.
References:
1.  Zarzycki, J., Schlichting, A., Strychalsky, N., Muller, M., Alber, B.E. and Fuchs, G. Mesaconyl-coenzyme A hydratase, a new enzyme of two central carbon metabolic pathways in bacteria. J. Bacteriol. 190 (2008) 1366–1374. [PMID: 18065535]
[EC 4.2.1.148 created 2014]
 
 
EC 4.2.1.149     
Accepted name: crotonobetainyl-CoA hydratase
Reaction: L-carnitinyl-CoA = (E)-4-(trimethylammonio)but-2-enoyl-CoA + H2O
Glossary: L-carnitinyl-CoA = (3R)-3-hydroxy-4-(trimethylammonio)butanoyl-CoA
(E)-4-(trimethylammonio)but-2-enoyl-CoA = crotonobetainyl-CoA
Other name(s): CaiD; L-carnityl-CoA dehydratase
Systematic name: L-carnitinyl-CoA hydro-lyase [(E)-4-(trimethylammonio)but-2-enoyl-CoA-forming]
Comments: The enzyme is also able to use crotonyl-CoA as substrate, with low efficiency [2].
References:
1.  Engemann, C., Elssner, T. and Kleber, H.P. Biotransformation of crotonobetaine to L-(–)-carnitine in Proteus sp. Arch. Microbiol. 175 (2001) 353–359. [PMID: 11409545]
2.  Elssner, T., Engemann, C., Baumgart, K. and Kleber, H.P. Involvement of coenzyme A esters and two new enzymes, an enoyl-CoA hydratase and a CoA-transferase, in the hydration of crotonobetaine to L-carnitine by Escherichia coli. Biochemistry 40 (2001) 11140–11148. [PMID: 11551212]
3.  Engemann, C., Elssner, T., Pfeifer, S., Krumbholz, C., Maier, T. and Kleber, H.P. Identification and functional characterisation of genes and corresponding enzymes involved in carnitine metabolism of Proteus sp. Arch. Microbiol. 183 (2005) 176–189. [PMID: 15731894]
[EC 4.2.1.149 created 2014]
 
 
EC 4.2.1.150     
Accepted name: short-chain-enoyl-CoA hydratase
Reaction: a short-chain (3S)-3-hydroxyacyl-CoA = a short-chain trans-2-enoyl-CoA + H2O
Other name(s): 3-hydroxybutyryl-CoA dehydratase; crotonase; crt (gene name)
Systematic name: short-chain-(3S)-3-hydroxyacyl-CoA hydro-lyase
Comments: The enzyme from the bacterium Clostridium acetobutylicum is part of the central fermentation pathway and plays a key role in the production of both acids and solvents. It is specific for short, C4-C6, chain length substrates and exhibits an extremely high turnover number for crotonyl-CoA. cf. EC 4.2.1.17, enoyl-CoA hydratase and EC 4.2.1.74, long-chain-enoyl-CoA hydratase.
References:
1.  Waterson, R.M., Castellino, F.J., Hass, G.M. and Hill, R.L. Purification and characterization of crotonase from Clostridium acetobutylicum. J. Biol. Chem. 247 (1972) 5266–5271. [PMID: 5057466]
2.  Waterson, R.M. and Conway, R.S. Enoyl-CoA hydratases from Clostridium acetobutylicum and Escherichia coli. Methods Enzymol. 71 Pt C (1981) 421–430. [PMID: 7024731]
3.  Boynton, Z.L., Bennet, G.N. and Rudolph, F.B. Cloning, sequencing, and expression of clustered genes encoding β-hydroxybutyryl-coenzyme A (CoA) dehydrogenase, crotonase, and butyryl-CoA dehydrogenase from Clostridium acetobutylicum ATCC 824. J. Bacteriol. 178 (1996) 3015–3024. [PMID: 8655474]
[EC 4.2.1.150 created 2014]
 
 
EC 4.2.1.151     
Accepted name: chorismate dehydratase
Reaction: chorismate = 3-[(1-carboxyvinyl)oxy]benzoate + H2O
Other name(s): MqnA
Systematic name: chorismate hydro-lyase (3-[(1-carboxyvinyl)oxy]benzoate-forming)
Comments: The enzyme, found in several bacterial species, is part of the futalosine pathway for menaquinone biosynthesis.
References:
1.  Mahanta, N., Fedoseyenko, D., Dairi, T. and Begley, T.P. Menaquinone biosynthesis: formation of aminofutalosine requires a unique radical SAM enzyme. J. Am. Chem. Soc. 135 (2013) 15318–15321. [PMID: 24083939]
[EC 4.2.1.151 created 2014]
 
 
EC 4.2.1.152     
Accepted name: hydroperoxy icosatetraenoate dehydratase
Reaction: a hydroperoxyicosatetraenoate = an oxoicosatetraenoate + H2O
Glossary: (12R)-HPETE = (5Z,8Z,10E,12R,14Z)-12-hydroperoxyicosa-5,8,10,14-tetraenoate
(12S)-HPETE = (5Z,8Z,10E,12S,14Z)-12-hydroperoxyicosa-5,8,10,14-tetraenoate
12-KETE = 12-oxo-ETE = (5Z,8Z,10E,14Z)-12-oxoicosa-5,8,10,14-tetraenoate
(8R)-HPETE = (5Z,8R,9E,11Z,14Z)-8-hydroperoxyicosa-5,9,11,14-tetraenoate
(15R)-HPETE = (5Z,8Z,11Z,13E,15R)-15-hydroperoxyicosa-5,8,11,13-tetraenoate
Other name(s): epidermal lipoxygenase-3 (ambiguous); eLOX3 (ambiguous)
Systematic name: hydroperoxyicosatetraenoate hydro-lyase (oxoicosatetraenoate-forming)
Comments: Binds Fe2+. The mammalian enzymes accept a range of hydroperoxyicosatetraenoates (HPETE). The human enzyme has highest activity with (12R)-HPETE, followed by (12S)-HPETE and (15R)-HPETE with much lower efficiency. The murine enzyme has highest activity with (8R)-HPETE followed by (8S)-HPETE. All HPETE isoforms are converted to the corresponding oxoicosatetraenoate forms (KETE) [2]. The enzymes also catalyse the reaction of EC 5.4.4.7, hydroperoxy icosatetraenoate isomerase.
References:
1.  Yu, Z., Schneider, C., Boeglin, W.E., Marnett, L.J. and Brash, A.R. The lipoxygenase gene ALOXE3 implicated in skin differentiation encodes a hydroperoxide isomerase. Proc. Natl. Acad. Sci. USA 100 (2003) 9162–9167. [PMID: 12881489]
2.  Yu, Z., Schneider, C., Boeglin, W.E. and Brash, A.R. Human and mouse eLOX3 have distinct substrate specificities: implications for their linkage with lipoxygenases in skin. Arch. Biochem. Biophys. 455 (2006) 188–196. [PMID: 17045234]
3.  Zheng, Y. and Brash, A.R. Dioxygenase activity of epidermal lipoxygenase-3 unveiled: typical and atypical features of its catalytic activity with natural and synthetic polyunsaturated fatty acids. J. Biol. Chem. 285 (2010) 39866–39875. [PMID: 20921226]
[EC 4.2.1.152 created 2014]
 
 
EC 4.2.1.153     
Accepted name: 3-methylfumaryl-CoA hydratase
Reaction: (S)-citramalyl-CoA = 3-methylfumaryl-CoA + H2O
Glossary: (S)-citramalyl-CoA = (3S)-3-carboxy-3-hydroxybutanoyl-CoA
3-methylfumaryl-CoA = (E)-3-carboxybut-2-enoyl-CoA
Other name(s): Meh; mesaconyl-C4-CoA hydratase; mesaconyl-coenzyme A hydratase (ambiguous)
Systematic name: (S)-citramalyl-CoA hydro-lyase (3-methylfumaryl-CoA-forming)
Comments: The enzyme from the bacterium Chloroflexus aurantiacus is part of the 3-hydroxypropanoate cycle for carbon assimilation.
References:
1.  Zarzycki, J., Brecht, V., Muller, M. and Fuchs, G. Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2 fixation cycle in Chloroflexus aurantiacus. Proc. Natl. Acad. Sci. USA 106 (2009) 21317–21322. [PMID: 19955419]
[EC 4.2.1.153 created 2014]
 
 
EC 4.2.1.154     
Accepted name: tetracenomycin F2 cyclase
Reaction: tetracenomycin F2 = tetracenomycin F1 + H2O
Glossary: tetracenomycin F1 = 3,8,10,12-tetrahydroxy-1-methyl-11-oxo-6,11-dihydro-2-tetracenecarboxylate = 6,11-dihydro-3,8,10,12-tetrahydroxy-1-methyl-11-oxonaphthacene-2-carboxylate
tetracenomycin F2 = (3E)-4-(3-acetyl-4,5,7-trihydroxy-10-oxo-9,10-dihydroanthracen-2-yl)-3-hydroxybut-3-enoate
Other name(s): tcmI (gene name)
Systematic name: tetracenomycin F2 hydro-lyase (tetracenomycin-F1-forming)
Comments: The enzyme is involved in biosynthesis of the anthracycline antibiotic tetracenomycin C by the bacterium Streptomyces glaucescens.
References:
1.  Shen, B. and Hutchinson, C.R. Tetracenomycin F2 cyclase: intramolecular aldol condensation in the biosynthesis of tetracenomycin C in Streptomyces glaucescens. Biochemistry 32 (1993) 11149–11154. [PMID: 8218177]
2.  Thompson, T.B., Katayama, K., Watanabe, K., Hutchinson, C.R. and Rayment, I. Structural and functional analysis of tetracenomycin F2 cyclase from Streptomyces glaucescens. A type II polyketide cyclase. J. Biol. Chem. 279 (2004) 37956–37963. [PMID: 15231835]
[EC 4.2.1.154 created 2014]
 
 
EC 4.2.1.155     
Accepted name: (methylthio)acryloyl-CoA hydratase
Reaction: 3-(methylsulfanyl)acryloyl-CoA + 2 H2O = acetaldehyde + methanethiol + CoA + CO2 (overall reaction)
(1a) 3-(methylsulfanyl)acryloyl-CoA + H2O = 3-hydroxy-3-(methylsulfanyl)propanoyl-CoA
(1b) 3-hydroxy-3-(methylsulfanyl)propanoyl-CoA = 3-oxopropanoyl-CoA + methanethiol
(1c) 3-oxopropanoyl-CoA + H2O = 3-oxopropanoate + CoA
(1d) 3-oxopropanoate = acetaldehyde + CO2
Glossary: 3-(methylsulfanyl)acryloyl-CoA = 3-(methylsulfanyl)prop-2-enoyl-CoA
Other name(s): DmdD
Systematic name: 3-(methylsulfanyl)prop-2-enoyl-CoA hydro-lyase (acetaldehyde-forming)
Comments: The enzyme is involved in the degradation of 3-(dimethylsulfonio)propanoate, an osmolyte produced by marine phytoplankton. Isolated from the bacterium Ruegeria pomeroyi.
References:
1.  Tan, D., Crabb, W.M., Whitman, W.B. and Tong, L. Crystal structure of DmdD, a crotonase superfamily enzyme that catalyzes the hydration and hydrolysis of methylthioacryloyl-CoA. PLoS One 8:e63870 (2013). [PMID: 23704947]
[EC 4.2.1.155 created 2015]
 
 
EC 4.2.1.156     
Accepted name: L-talarate dehydratase
Reaction: L-altarate = 5-dehydro-4-deoxy-D-glucarate + H2O
Glossary: L-altrarate = L-talarate = (2R,3R,4S,5R)-2,3,4,5-tetrahydroxyhexanedioate
Other name(s): L-talarate hydro-lyase
Systematic name: L-altarate hydro-lyase (5-dehydro-4-deoxy-D-glucarate-forming)
Comments: Requires Mg2+. The enzyme, isolated from the bacteria Salmonella typhimurium and Polaromonas sp. JS666, also has activity with galactarate (cf. EC 4.2.1.42, galactarate dehydratase).
References:
1.  Yew, W.S., Fedorov, A.A., Fedorov, E.V., Almo, S.C. and Gerlt, J.A. Evolution of enzymatic activities in the enolase superfamily: L-talarate/galactarate dehydratase from Salmonella typhimurium LT2. Biochemistry 46 (2007) 9564–9577. [PMID: 17649980]
[EC 4.2.1.156 created 2015]
 
 
EC 4.2.1.157     
Accepted name: (R)-2-hydroxyisocaproyl-CoA dehydratase
Reaction: (R)-2-hydroxy-4-methylpentanoyl-CoA = 4-methylpent-2-enoyl-CoA + H2O
Other name(s): 2-hydroxyisocaproyl-CoA dehydratase; HadBC
Systematic name: (R)-2-hydroxy-4-methylpentanoyl-CoA hydro-lyase
Comments: The enzyme, isolated from the bacterium Peptoclostridium difficile, is involved in the reductive branch of L-leucine fermentation. It catalyses an α/β-dehydration, which depends on the reductive formation of ketyl radicals on the substrate generated by injection of a single electron from the ATP-dependent activator protein HadI.
References:
1.  Kim, J., Darley, D. and Buckel, W. 2-Hydroxyisocaproyl-CoA dehydratase and its activator from Clostridium difficile. FEBS J. 272 (2005) 550–561. [PMID: 15654892]
2.  Knauer, S.H., Buckel, W. and Dobbek, H. Structural basis for reductive radical formation and electron recycling in (R)-2-hydroxyisocaproyl-CoA dehydratase. J. Am. Chem. Soc. 133 (2011) 4342–4347. [PMID: 21366233]
[EC 4.2.1.157 created 2015]
 
 
EC 4.2.1.158     
Accepted name: galactarate dehydratase (D-threo-forming)
Reaction: galactarate = (2S,3R)-2,3-dihydroxy-5-oxohexanedioate + H2O
Glossary: galactarate = (2R,3S,4R,5S)-2,3,4,5-tetrahydroxyhexanedioate
(2S,3R)-2,3-dihydroxy-5-oxohexanedioate = 3-deoxy-D-threo-hex-2-ulosarate
Systematic name: galactarate hydro-lyase (3-deoxy-D-threo-hex-2-ulosarate-forming)
Comments: The enzyme has been characterized from the bacterium Oceanobacillus iheyensis. cf. EC 4.2.1.42, galactarate dehydratase.
References:
1.  Rakus, J.F., Kalyanaraman, C., Fedorov, A.A., Fedorov, E.V., Mills-Groninger, F.P., Toro, R., Bonanno, J., Bain, K., Sauder, J.M., Burley, S.K., Almo, S.C., Jacobson, M.P. and Gerlt, J.A. Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis. Biochemistry 48 (2009) 11546–11558. [PMID: 19883118]
[EC 4.2.1.158 created 2015]
 
 
EC 4.2.1.159     
Accepted name: dTDP-4-dehydro-6-deoxy-α-D-glucopyranose 2,3-dehydratase
Reaction: dTDP-4-dehydro-6-deoxy-α-D-glucopyranose = dTDP-3,4-didehydro-2,6-dideoxy-α-D-glucose + H2O (overall reaction)
(1a) dTDP-4-dehydro-6-deoxy-α-D-glucopyranose = dTDP-2,6-dideoxy-D-glycero-hex-2-enos-4-ulose + H2O
(1b) dTDP-2,6-dideoxy-D-glycero-hex-2-enos-4-ulose = dTDP-3,4-didehydro-2,6-dideoxy-α-D-glucose (spontaneous)
Other name(s): jadO (gene name); evaA (gene name); megBVI (gene name); eryBV (gene name); mtmV (gene name); oleV (gene name); spnO (gene name); TDP-4-keto-6-deoxy-D-glucose 2,3-dehydratase; dTDP-4-dehydro-6-deoxy-α-D-glucopyranose hydro-lyase (dTDP-(2R,6S)-2,4-dihydroxy-6-methyl-2,6-dihydropyran-3-one-forming)
Systematic name: dTDP-4-dehydro-6-deoxy-α-D-glucopyranose hydro-lyase (dTDP-2,6-dideoxy-D-glycero-hex-2-enos-4-ulose-forming)
Comments: The enzyme participates in the biosynthesis of several deoxysugars, including β-L-4-epi-vancosamine, α-L-megosamine, L- and D-olivose, D-oliose, D-mycarose, forosamine and β-L-digitoxose. In vitro the intermediate can undergo a spontaneous decomposition to maltol [2,3].
References:
1.  Aguirrezabalaga, I., Olano, C., Allende, N., Rodriguez, L., Brana, A.F., Mendez, C. and Salas, J.A. Identification and expression of genes involved in biosynthesis of L-oleandrose and its intermediate L-olivose in the oleandomycin producer Streptomyces antibioticus. Antimicrob. Agents Chemother. 44 (2000) 1266–1275. [PMID: 10770761]
2.  Chen, H., Thomas, M.G., Hubbard, B.K., Losey, H.C., Walsh, C.T. and Burkart, M.D. Deoxysugars in glycopeptide antibiotics: enzymatic synthesis of TDP-L-epivancosamine in chloroeremomycin biosynthesis. Proc. Natl. Acad. Sci. USA 97 (2000) 11942–11947. [PMID: 11035791]
3.  Gonzalez, A., Remsing, L.L., Lombo, F., Fernandez, M.J., Prado, L., Brana, A.F., Kunzel, E., Rohr, J., Mendez, C. and Salas, J.A. The mtmVUC genes of the mithramycin gene cluster in Streptomyces argillaceus are involved in the biosynthesis of the sugar moieties. Mol. Gen. Genet. 264 (2001) 827–835. [PMID: 11254130]
4.  Wang, L., White, R.L. and Vining, L.C. Biosynthesis of the dideoxysugar component of jadomycin B: genes in the jad cluster of Streptomyces venezuelae ISP5230 for L-digitoxose assembly and transfer to the angucycline aglycone. Microbiology 148 (2002) 1091–1103. [PMID: 11932454]
5.  Hong, L., Zhao, Z., Melancon, C.E., 3rd, Zhang, H. and Liu, H.W. In vitro characterization of the enzymes involved in TDP-D-forosamine biosynthesis in the spinosyn pathway of Saccharopolyspora spinosa. J. Am. Chem. Soc. 130 (2008) 4954–4967. [PMID: 18345667]
6.  Useglio, M., Peiru, S., Rodriguez, E., Labadie, G.R., Carney, J.R. and Gramajo, H. TDP-L-megosamine biosynthesis pathway elucidation and megalomicin a production in Escherichia coli. Appl. Environ. Microbiol. 76 (2010) 3869–3877. [PMID: 20418422]
[EC 4.2.1.159 created 2015]
 
 
EC 4.2.1.160     
Accepted name: 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one isomerase/dehydratase
Reaction: 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one = 7,8-dihydroneopterin 3′-phosphate + H2O
Systematic name: 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one cyclohydrolase
Comments: The enzyme participates in a folate biosynthesis pathway in Chlamydia.
References:
1.  Adams, N.E., Thiaville, J.J., Proestos, J., Juarez-Vazquez, A.L., McCoy, A.J., Barona-Gomez, F., Iwata-Reuyl, D., de Crecy-Lagard, V. and Maurelli, A.T. Promiscuous and adaptable enzymes fill "holes" in the tetrahydrofolate pathway in Chlamydia species. MBio 5 (2014) e01378. [PMID: 25006229]
[EC 4.2.1.160 created 2015]
 
 
EC 4.2.1.161     
Accepted name: bisanhydrobacterioruberin hydratase
Reaction: bacterioruberin = bisanhydrobacterioruberin + 2 H2O (overall reaction)
(1a) bacterioruberin = monoanhydrobacterioruberin + H2O
(1b) monoanhydrobacterioruberin = bisanhydrobacterioruberin + H2O
Glossary: bisanhydrobacterioruberin = 2,2′-bis(3-methylbut-2-enyl)-3,4,3′,4′-tetradehydro-1,2,1′,2′-tetrahydro-ψ,ψ-carotene-1,1′-diol
monoanhydrobacterioruberin = 2-(3-hydroxy-3-methylbutyl)-2′-(3-methylbut-2-enyl)-3,4,3′,4′-tetradehydro-1,2,1′,2′-tetrahydro-ψ,ψ-carotene-1,1′-diol
Other name(s): CruF; C50 carotenoid 2′′,3′′-hydratase
Systematic name: bacterioruberin hydro-lyase (bisanhydrobacterioruberin-forming)
Comments: The enzyme, isolated from the archaeon Haloarcula japonica, is involved in the biosynthesis of the C50 carotenoid bacterioruberin. In this pathway it catalyses the introduction of hydroxyl groups to C3′′ and C3′′′ of bisanhydrobacterioruberin to generate bacterioruberin.
References:
1.  Yang, Y., Yatsunami, R., Ando, A., Miyoko, N., Fukui, T., Takaichi, S. and Nakamura, S. Complete biosynthetic pathway of the C50 carotenoid bacterioruberin from lycopene in the extremely halophilic archaeon Haloarcula japonica. J. Bacteriol. 197 (2015) 1614–1623. [PMID: 25712483]
[EC 4.2.1.161 created 2015]
 
 
EC 4.2.1.162     
Accepted name: 6-deoxy-6-sulfo-D-gluconate dehydratase
Reaction: 6-deoxy-6-sulfo-D-gluconate = 2-dehydro-3,6-dideoxy-6-sulfo-D-gluconate + H2O
Other name(s): SG dehydratase
Systematic name: 6-deoxy-6-sulfo-D-gluconate hydro-lyase (2-dehydro-3,6-dideoxy-6-sulfo-D-gluconate-forming)
Comments: The enzyme, characterized from the bacterium Pseudomonas putida SQ1, participates in a sulfoquinovose degradation pathway.
References:
1.  Felux, A.K., Spiteller, D., Klebensberger, J. and Schleheck, D. Entner-Doudoroff pathway for sulfoquinovose degradation in Pseudomonas putida SQ1. Proc. Natl. Acad. Sci. USA 112 (2015) E4298–E4305. [PMID: 26195800]
[EC 4.2.1.162 created 2016]
 
 
EC 4.2.1.163     
Accepted name: 2-oxo-hept-4-ene-1,7-dioate hydratase
Reaction: (4Z)-2-oxohept-4-enedioate + H2O = (4S)-4-hydroxy-2-oxoheptanedioate
Other name(s): HpcG
Systematic name: (4S)-4-hydroxy-2-oxoheptanedioate hydro-lyase [(4Z)-2-oxohept-4-enedioate-forming]
Comments: Requires Mg2+ [2]. Part of a 4-hydroxyphenylacetate degradation pathway in Escherichia coli C.
References:
1.  Burks, E.A., Johnson, W.H., Jr. and Whitman, C.P. Stereochemical and isotopic labeling studies of 2-oxo-hept-4-ene-1,7-dioate hydratase: evidence for an enzyme-catalyzed ketonization step in the hydration reaction. J. Am. Chem. Soc. 120 (1998) 7665–7675.
2.  Izumi, A., Rea, D., Adachi, T., Unzai, S., Park, S.Y., Roper, D.I. and Tame, J.R. Structure and mechanism of HpcG, a hydratase in the homoprotocatechuate degradation pathway of Escherichia coli. J. Mol. Biol. 370 (2007) 899–911. [PMID: 17559873]
[EC 4.2.1.163 created 2016]
 
 
EC 4.2.1.164     
Accepted name: dTDP-4-dehydro-2,6-dideoxy-D-glucose 3-dehydratase
Reaction: dTDP-4-dehydro-2,6-dideoxy-α-D-glucose + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ = dTDP-4-dehydro-2,3,6-trideoxy-α-D-hexopyranose + H2O + 2 oxidized ferredoxin [iron-sulfur] cluster
Other name(s): SpnQ; TDP-4-keto-2,6-dideoxy-D-glucose 3-dehydrase
Systematic name: dTDP-4-dehydro-2,6-dideoxy-α-D-glucose hydro-lyase (dTDP-2,3,6-trideoxy-α-D-hexopyranose-forming)
Comments: A pyridoxal 5′-phosphate protein. The enzyme, isolated from the bacterium Saccharopolyspora spinosa, participates in the biosynthesis of forosamine. Requires ferredoxin/ferredoxin reductase or flavodoxin/flavodoxin reductase [1].
References:
1.  Hong, L., Zhao, Z. and Liu, H.W. Characterization of SpnQ from the spinosyn biosynthetic pathway of Saccharopolyspora spinosa: mechanistic and evolutionary implications for C-3 deoxygenation in deoxysugar biosynthesis. J. Am. Chem. Soc. 128 (2006) 14262–14263. [PMID: 17076492]
2.  Hong, L., Zhao, Z., Melancon, C.E., 3rd, Zhang, H. and Liu, H.W. In vitro characterization of the enzymes involved in TDP-D-forosamine biosynthesis in the spinosyn pathway of Saccharopolyspora spinosa. J. Am. Chem. Soc. 130 (2008) 4954–4967. [PMID: 18345667]
[EC 4.2.1.164 created 2016]
 
 
EC 4.2.1.165     
Accepted name: chlorophyllide a 31-hydratase
Reaction: (1) 3-devinyl-3-(1-hydroxyethyl)chlorophyllide a = chlorophyllide a + H2O
(2) 3-deacetyl-3-(1-hydroxyethyl)bacteriochlorophyllide a = 3-deacetyl-3-vinylbacteriochlorophyllide a + H2O
Other name(s): bchF (gene name)
Systematic name: chlorophyllide-a 31-hydro-lyase
Comments: The enzyme, together with EC 1.3.7.15, chlorophyllide-a reductase, and EC 1.1.1.396, bacteriochlorophyllide-a dehydrogenase, is involved in the conversion of chlorophyllide a to bacteriochlorophyllide a. The enzymes can act in multiple orders, resulting in the formation of different intermediates, but the final product of the cumulative action of the three enzymes is always bacteriochlorophyllide a. The enzyme catalyses the hydration of a vinyl group on ring A, converting it to a hydroxyethyl group.
References:
1.  Pudek, M.R. and Richards, W.R. A possible alternate pathway of bacteriochlorophyll biosynthesis in a mutant of Rhodopseudomonas sphaeroides. Biochemistry 14 (1975) 3132–3137. [PMID: 1080053]
2.  Burke, D.H., Alberti, M. and Hearst, J.E. bchFNBH bacteriochlorophyll synthesis genes of Rhodobacter capsulatus and identification of the third subunit of light-independent protochlorophyllide reductase in bacteria and plants. J. Bacteriol. 175 (1993) 2414–2422. [PMID: 8385667]
3.  Lange, C., Kiesel, S., Peters, S., Virus, S., Scheer, H., Jahn, D. and Moser, J. Broadened substrate specificity of 3-hydroxyethyl bacteriochlorophyllide a dehydrogenase (BchC) indicates a new route for the biosynthesis of bacteriochlorophyll a. J. Biol. Chem. 290 (2015) 19697–19709. [PMID: 26088139]
4.  Harada, J., Teramura, M., Mizoguchi, T., Tsukatani, Y., Yamamoto, K. and Tamiaki, H. Stereochemical conversion of C3-vinyl group to 1-hydroxyethyl group in bacteriochlorophyll c by the hydratases BchF and BchV: adaptation of green sulfur bacteria to limited-light environments. Mol. Microbiol. 98 (2015) 1184–1198. [PMID: 26331578]
[EC 4.2.1.165 created 2016]
 
 
EC 4.2.1.166     
Accepted name: phosphinomethylmalate isomerase
Reaction: 2-(hydroxyphosphonoylmethyl)malate = 3-(hydroxyphosphonoylmethyl)malate (overall reaction)
(1a) 2-(hydroxyphosphonoylmethyl)malate = 2-(phosphinatomethylidene)butanedioate + H2O
(1b) 2-(phosphinatomethylidene)butanedioate + H2O = 3-(hydroxyphosphonoylmethyl)malate
Glossary: 2-(hydroxyphosphonoylmethyl)malate = 2-hydroxy-2-(hydroxyphosphonoylmethyl)butanedioate
3-(hydroxyphosphonoylmethyl)malate = 2-hydroxy-3-(hydroxyphosphonoylmethyl)butanedioate
Other name(s): pmi (gene name)
Systematic name: 2-(phosphinomethyl)malate hydro-lyase [3-(phosphinomethyl)malate-forming]
Comments: The enzyme, characterized from the bacterium Streptomyces viridochromogenes, is involved in bialaphos biosynthesis. The enzyme from the bacterium Kitasatospora phosalacinea participates in the biosynthesis of the related compound phosalacine. Both compounds contain the nonproteinogenic amino acid L-phosphinothricin that acts as a potent inhibitor of EC 6.3.1.2, glutamine synthetase. The similar enzyme EC 4.2.1.3, aconitate hydratase, cannot catalyse this reaction.
References:
1.  Heinzelmann, E., Kienzlen, G., Kaspar, S., Recktenwald, J., Wohlleben, W. and Schwartz, D. The phosphinomethylmalate isomerase gene pmi, encoding an aconitase-like enzyme, is involved in the synthesis of phosphinothricin tripeptide in Streptomyces viridochromogenes. Appl. Environ. Microbiol. 67 (2001) 3603–3609. [PMID: 11472937]
[EC 4.2.1.166 created 2016]
 
 
EC 4.2.1.167     
Accepted name: (R)-2-hydroxyglutaryl-CoA dehydratase
Reaction: (R)-2-hydroxyglutaryl-CoA = (E)-glutaconyl-CoA + H2O
Other name(s): hgdAB (gene names)
Systematic name: (R)-2-hydroxyglutaryl-CoA hydro-lyase ((E)-glutaconyl-CoA-forming)
Comments: The enzymes from the bacteria Acidaminococcus fermentans and Clostridium symbiosum are involved in the fermentation of L-glutamate. The enzyme contains [4F-4S] clusters, FMNH2 and riboflavin. It must be activated by an activator protein. Once activated, it can catalyse many turnovers.
References:
1.  Buckel, W. The reversible dehydration of (R)-2-hydroxyglutarate to (E)-glutaconate. Eur. J. Biochem. 106 (1980) 439–447. [PMID: 7398622]
2.  Schweiger, G., Dutscho, R. and Buckel, W. Purification of 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. An iron-sulfur protein. Eur. J. Biochem. 169 (1987) 441–448. [PMID: 3691501]
3.  Müller, U. and Buckel, W. Activation of (R)-2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. Eur. J. Biochem. 230 (1995) 698–704. [PMID: 7607244]
4.  Hans, M., Sievers, J., Muller, U., Bill, E., Vorholt, J.A., Linder, D. and Buckel, W. 2-hydroxyglutaryl-CoA dehydratase from Clostridium symbiosum. Eur. J. Biochem. 265 (1999) 404–414. [PMID: 10491198]
5.  Locher, K.P., Hans, M., Yeh, A.P., Schmid, B., Buckel, W. and Rees, D.C. Crystal structure of the Acidaminococcus fermentans 2-hydroxyglutaryl-CoA dehydratase component A. J. Mol. Biol. 307 (2001) 297–308. [PMID: 11243821]
6.  Parthasarathy, A., Pierik, A.J., Kahnt, J., Zelder, O. and Buckel, W. Substrate specificity of 2-hydroxyglutaryl-CoA dehydratase from Clostridium symbiosum: toward a bio-based production of adipic acid. Biochemistry 50 (2011) 3540–3550. [PMID: 21434666]
[EC 4.2.1.167 created 2016]
 
 
EC 4.2.1.168     
Accepted name: GDP-4-dehydro-6-deoxy-α-D-mannose 3-dehydratase
Reaction: GDP-4-dehydro-α-D-rhamnose + L-glutamate = GDP-4-dehydro-3,6-dideoxy-α-D-mannose + 2-oxoglutarate + NH3 (overall reaction)
(1a) GDP-4-dehydro-α-D-rhamnose + L-glutamate = 2-GDP-[(2S,3S,6R)-5-amino-6-methyl-3,6-dihydro-2H-pyran-3-ol] + 2-oxoglutarate + H2O
(1b) 2-GDP-[(2S,3S,6R)-5-amino-6-methyl-3,6-dihydro-2H-pyran-3-ol] = 2-GDP-[(2S,3S,6R)-5-imino-6-methyloxan-3-ol] (spontaneous)
(1c) GDP-2-[(2S,3S,6R)-5-imino-6-methyloxan-3-ol] + H2O = GDP-4-dehydro-3,6-dideoxy-α-D-mannose + NH3 (spontaneous)
Glossary: GDP-4-dehydro-α-D-rhamnose = GDP-4-dehydro-6-deoxy-α-D-mannose
Other name(s): colD (gene name)
Systematic name: GDP-4-dehydro-α-D-rhamnose 3-hydro-lyase
Comments: This enzyme, involved in β-L-colitose biosynthesis, is a unique vitamin-B6-dependent enzyme. In the first step of catalysis, the bound pyridoxal phosphate (PLP) cafactor is transaminated to the pyridoxamine 5′-phosphate (PMP) form of vitamin B6, using L-glutamate as the amino group donor. The PMP cofactor then forms a Schiff base with the sugar substrate and the resulting adduct undergoes a 1,4-dehydration to eliminate the 3-OH group. Hydrolysis of the product from the enzyme restores the PLP cofactor and results in the release of an unstable enamine intermediate. This intermediate tautomerizes to form an imine form, which hydrolyses spontaneously, releasing ammonia and forming the final product.
References:
1.  Alam, J., Beyer, N. and Liu, H.W. Biosynthesis of colitose: expression, purification, and mechanistic characterization of GDP-4-keto-6-deoxy-D-mannose-3-dehydrase (ColD) and GDP-L-colitose synthase (ColC). Biochemistry 43 (2004) 16450–16460. [PMID: 15610039]
2.  Cook, P.D. and Holden, H.M. A structural study of GDP-4-keto-6-deoxy-D-mannose-3-dehydratase: caught in the act of geminal diamine formation. Biochemistry 46 (2007) 14215–14224. [PMID: 17997582]
[EC 4.2.1.168 created 2016]
 
 
EC 4.2.1.169     
Accepted name: 3-vinyl bacteriochlorophyllide d 31-hydratase
Reaction: a 3-(1-hydroxyethyl) bacteriochlorophyllide d = a 3-vinyl bacteriochlorophyllide d + H2O
Other name(s): bchV (gene name)
Systematic name: 3-vinylbacteriochlorophyllide-d 31-hydro-lyase
Comments: This enzyme, found in green sulfur bacteria (Chlorobiaceae) and green flimentous bacteria (Chloroflexaceae), is involved in the biosynthesis of bacteriochlorophylls c, d and e. It acts in the direction of hydration, and the hydroxyl group that is formed is essential for the ability of the resulting bacteriochlorophylls to self-aggregate in the chlorosomes, unique light-harvesting antenna structures found in these organisms. The product is formed preferentially in the (R)-configuration.
References:
1.  Frigaard, N.U., Chew, A.G., Li, H., Maresca, J.A. and Bryant, D.A. Chlorobium tepidum: insights into the structure, physiology, and metabolism of a green sulfur bacterium derived from the complete genome sequence. Photosynth. Res. 78 (2003) 93–117. [PMID: 16245042]
2.  Harada, J., Teramura, M., Mizoguchi, T., Tsukatani, Y., Yamamoto, K. and Tamiaki, H. Stereochemical conversion of C3-vinyl group to 1-hydroxyethyl group in bacteriochlorophyll c by the hydratases BchF and BchV: adaptation of green sulfur bacteria to limited-light environments. Mol. Microbiol. 98 (2015) 1184–1198. [PMID: 26331578]
[EC 4.2.1.169 created 2016]
 
 
EC 4.2.1.170     
Accepted name: 2-(ω-methylthio)alkylmalate dehydratase
Reaction: (1) a 2-[(ω-methylsulfanyl)alkyl]malate = a 2-[(ω-methylsulfanyl)alkyl]maleate + H2O
(2) a 3-[(ω-methylsulfanyl)alkyl]malate = a 2-[(ω-methylsulfanyl)alkyl]maleate + H2O
Other name(s): IPMI (gene name); 2-[(ω-methylthio)alkyl]malate hydro-lyase (2-[(ω-methylthio)alkyl]maleate-forming)
Systematic name: 2-[(ω-methylsulfanyl)alkyl]malate hydro-lyase (2-[(ω-methylsulfanyl)alkyl]maleate-forming)
Comments: The enzyme, characterized from the plant Arabidopsis thaliana, is involved in the L-methionine side-chain elongation pathway, forming substrates for the biosynthesis of aliphatic glucosinolates. By catalysing a dehydration of a 2-[(ω-methylsulfanyl)alkyl]maleate, followed by a hydration at a different position, the enzyme achieves the isomerization of its substrates. The enzyme is a heterodimer comprising a large and a small subunits. The large subunit can also bind to an alternative small subunit, forming EC 4.2.1.33, 3-isopropylmalate dehydratase, which participates in L-leucine biosynthesis.
References:
1.  Knill, T., Reichelt, M., Paetz, C., Gershenzon, J. and Binder, S. Arabidopsis thaliana encodes a bacterial-type heterodimeric isopropylmalate isomerase involved in both Leu biosynthesis and the Met chain elongation pathway of glucosinolate formation. Plant Mol. Biol. 71 (2009) 227–239. [PMID: 19597944]
[EC 4.2.1.170 created 2016]
 
 
EC 4.2.1.171     
Accepted name: cis-L-3-hydroxyproline dehydratase
Reaction: cis-3-hydroxy-L-proline = 1-pyrroline-2-carboxylate + H2O
Glossary: 1-pyrroline-2-carboxylate = 4,5-dihydro-3H-pyrrole-2-carboxylate
Other name(s): cis-L-3-hydroxyproline hydro-lyase; c3LHypD
Systematic name: cis-3-hydroxy-L-proline hydro-lyase (1-pyrroline-2-carboxylate-forming)
References:
1.  Zhang, X., Kumar, R., Vetting, M.W., Zhao, S., Jacobson, M.P., Almo, S.C. and Gerlt, J.A. A unique cis-3-hydroxy-L-proline dehydratase in the enolase superfamily. J. Am. Chem. Soc. 137 (2015) 1388–1391. [PMID: 25608448]
[EC 4.2.1.171 created 2017]
 
 
EC 4.2.1.172     
Accepted name: trans-4-hydroxy-L-proline dehydratase
Reaction: trans-4-hydroxy-L-proline = (S)-1-pyrroline-5-carboxylate + H2O
Glossary: 1-pyrroline = 3,4-dihydro-2H-pyrrole
Systematic name: trans-4-hydroxy-L-proline hydro-lyase
Comments: The enzyme has been characterized from the bacterium Peptoclostridium difficile. The active form contains a glycyl radical that is generated by a dedicated activating enzyme via chemistry involving S-adenosyl-L-methionine (SAM) and a [4Fe-4S] cluster.
References:
1.  Levin, B.J., Huang, Y.Y., Peck, S.C., Wei, Y., Martinez-Del Campo, A., Marks, J.A., Franzosa, E.A., Huttenhower, C. and Balskus, E.P. A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-L-proline. Science 355 (2017) . [PMID: 28183913]
[EC 4.2.1.172 created 2017]
 
 
EC 4.2.1.173     
Accepted name: ent-8α-hydroxylabd-13-en-15-yl diphosphate synthase
Reaction: ent-8α-hydroxylabd-13-en-15-yl diphosphate = geranylgeranyl diphosphate + H2O
Other name(s): SmCPS4
Systematic name: geranylgeranyl-diphosphate hydro-lyase (ent-8α-hydroxylabd-13-en-15-yl diphosphate forming)
Comments: Isolated from the plant Salvia miltiorrhiza (red sage).
References:
1.  Cui, G., Duan, L., Jin, B., Qian, J., Xue, Z., Shen, G., Snyder, J.H., Song, J., Chen, S., Huang, L., Peters, R.J. and Qi, X. Functional divergence of diterpene syntheses in the medicinal plant Salvia miltiorrhiza. Plant Physiol. 169 (2015) 1607–1618. [PMID: 26077765]
[EC 4.2.1.173 created 2017]
 
 
EC 4.2.1.174     
Accepted name: peregrinol diphosphate synthase
Reaction: peregrinol diphosphate = geranylgeranyl diphosphate + H2O
Glossary: peregrinol diphosphate = (13E)-9-hydroxy-8α-labda-13-en-15-yl diphosphate
Other name(s): MvCPS1
Systematic name: geranylgeranyl-diphosphate hydro-lyase (peregrinol diphosphate forming)
Comments: Isolated from the plant Marrubium vulgare (white horehound). Involved in marrubiin biosynthesis.
References:
1.  Zerbe, P., Chiang, A., Dullat, H., O'Neil-Johnson, M., Starks, C., Hamberger, B. and Bohlmann, J. Diterpene synthases of the biosynthetic system of medicinally active diterpenoids in Marrubium vulgare. Plant J. 79 (2014) 914–927. [PMID: 24990389]
[EC 4.2.1.174 created 2017]
 
 
EC 4.2.1.175     
Accepted name: (R)-3-(aryl)lactoyl-CoA dehydratase
Reaction: (1) (R)-3-(phenyl)lactoyl-CoA = (E)-cinnamoyl-CoA + H2O
(2) (R)-3-(4-hydroxyphenyl)lactoyl-CoA = (E)-4-coumaroyl-CoA + H2O
(3) (R)-3-(indol-3-yl)lactoyl-CoA = 3-(indol-3-yl)acryloyl-CoA + H2O
Other name(s): fldBC (gene names); (R)-phenyllactoyl-CoA dehydratase; aryllactyl-CoA dehydratase
Systematic name: (R)-3-(aryl)lactoyl-CoA hydro-lyase
Comments: The enzyme, found in some amino acid-fermenting anaerobic bacteria, participates in the fermentation pathways of L-phenylalanine, L-tyrosine, and L-tryptophan. It is a heterodimeric protein consisting of the FldB and FldC polypeptides, both of which contain an [4Fe-4S] cluster, and forms a complex with EC 2.8.3.17, 3-(aryl)acryloyl-CoA:(R)-3-(aryl)lactate CoA-transferase (FldA). In order to catalyse the reaction, the enzyme requires one high-energy electron that transiently reduces the electrophilic thiol ester carbonyl of the substrate to a nucleophilic ketyl radical anion, facilitating the elimination of the hydroxyl group. This electron, which is provided by by EC 5.6.1.9, (R)-2-hydroxyacyl-CoA dehydratase activating ATPase, needs to be supplied only once, before the first reaction takes place, as it is regenerated at the end of each reaction cycle. The enzyme acts on (R)-3-(aryl)lactoyl-CoAs produced by FldA, and regenerates the CoA donors used by that enzyme.
References:
1.  Dickert, S., Pierik, A.J., Linder, D. and Buckel, W. The involvement of coenzyme A esters in the dehydration of (R)-phenyllactate to (E)-cinnamate by Clostridium sporogenes. Eur. J. Biochem. 267 (2000) 3874–3884. [PMID: 10849007]
2.  Dickert, S., Pierik, A.J. and Buckel, W. Molecular characterization of phenyllactate dehydratase and its initiator from Clostridium sporogenes. Mol. Microbiol. 44 (2002) 49–60. [PMID: 11967068]
3.  Kim, J., Hetzel, M., Boiangiu, C.D. and Buckel, W. Dehydration of (R)-2-hydroxyacyl-CoA to enoyl-CoA in the fermentation of α-amino acids by anaerobic bacteria. FEMS Microbiol. Rev. 28 (2004) 455–468. [PMID: 15374661]
4.  Kim, J., Darley, D.J., Buckel, W. and Pierik, A.J. An allylic ketyl radical intermediate in clostridial amino-acid fermentation. Nature 452 (2008) 239–242. [PMID: 18337824]
5.  Dodd, D., Spitzer, M.H., Van Treuren, W., Merrill, B.D., Hryckowian, A.J., Higginbottom, S.K., Le, A., Cowan, T.M., Nolan, G.P., Fischbach, M.A. and Sonnenburg, J.L. A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites. Nature 551 (2017) 648–652. [PMID: 29168502]
[EC 4.2.1.175 created 2019]
 
 
EC 4.2.2.1     
Accepted name: hyaluronate lyase
Reaction: Cleaves hyaluronate chains at a β-D-GlcNAc-(1→4)-β-D-GlcA bond, ultimately breaking the polysaccharide down to 3-(4-deoxy-β-D-gluc-4-enuronosyl)-N-acetyl-D-glucosamine.
Other name(s): hyaluronidase (ambiguous); glucuronoglycosaminoglycan lyase (ambiguous); spreading factor; mucinase (ambiguous)
Systematic name: hyaluronate lyase
Comments: The enzyme catalyses the degradation of hyaluronan by a β-elimination reaction. Also acts on chondroitin. The product is more systematically known as 3-(4-deoxy-α-L-threo-hex-4-enopyranosyluronic acid)-2-acetamido-2-deoxy-D-glucose
References:
1.  Linker, A., Hoffman, P., Meyer, K., Sampson, P. and Korn, E.D. The formation of unsaturated disacharides from mucopoly-saccharides and their cleavage to α-keto acid by bacterial enzymes. J. Biol. Chem. 235 (1960) 3061. [PMID: 13762462]
2.  Meyer, K. and Rapport, M.M. Hyaluronidases. Adv. Enzymol. Relat. Subj. Biochem. 13 (1952) 199–236. [PMID: 14943668]
3.  Moran, F., Nasuno, S. and Starr, M.P. Extracellular and intracellular polygalacturonic acid trans-eliminases of Erwinia carotovora. Arch. Biochem. Biophys. 123 (1968) 298–306. [PMID: 5642600]
[EC 4.2.2.1 created 1961 as EC 4.2.99.1, transferred 1972 to EC 4.2.2.1, modified 2001]
 
 
EC 4.2.2.2     
Accepted name: pectate lyase
Reaction: Eliminative cleavage of (1→4)-α-D-galacturonan to give oligosaccharides with 4-deoxy-α-D-galact-4-enuronosyl groups at their non-reducing ends
Other name(s): polygalacturonic transeliminase; pectic acid transeliminase; polygalacturonate lyase; endopectin methyltranseliminase; pectate transeliminase; endogalacturonate transeliminase; pectic acid lyase; pectic lyase; α-1,4-D-endopolygalacturonic acid lyase; PGA lyase; PPase-N; endo-α-1,4-polygalacturonic acid lyase; polygalacturonic acid lyase; pectin trans-eliminase; Polygalacturonic acid trans-eliminase
Systematic name: (1→4)-α-D-galacturonan lyase
Comments: Favours pectate, the anion, over pectin, the methyl ester (which is the preferred substrate of EC 4.2.2.10, pectin lyase).
References:
1.  Albersheim, P. and Killias, U.