The Enzyme Database

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EC 1.1.1.41     
Accepted name: isocitrate dehydrogenase (NAD+)
Reaction: isocitrate + NAD+ = 2-oxoglutarate + CO2 + NADH
For diagram of the citric-acid cycle, click here
Glossary: isocitrate = (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate (previously known as threo-Ds-isocitrate)
Other name(s): isocitric dehydrogenase; β-ketoglutaric-isocitric carboxylase; isocitric acid dehydrogenase; NAD dependent isocitrate dehydrogenase; NAD isocitrate dehydrogenase; NAD-linked isocitrate dehydrogenase; NAD-specific isocitrate dehydrogenase; NAD isocitric dehydrogenase; isocitrate dehydrogenase (NAD); IDH (ambiguous); nicotinamide adenine dinucleotide isocitrate dehydrogenase
Systematic name: isocitrate:NAD+ oxidoreductase (decarboxylating)
Comments: Requires Mn2+ or Mg2+ for activity. Unlike EC 1.1.1.42, isocitrate dehydrogenase (NADP+), oxalosuccinate cannot be used as a substrate. In eukaryotes, isocitrate dehydrogenase exists in two forms: an NAD+-linked enzyme found only in mitochondria and displaying allosteric properties, and a non-allosteric, NADP+-linked enzyme that is found in both mitochondria and cytoplasm [7]. The enzyme from some species can also use NADP+ but much more slowly [9].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9001-58-5
References:
1.  Hathaway, J.A. and Atkinson, D.E. The effect of adenylic acid on yeast nicotinamide adenine dinucleotide isocitrate dehydrogenase, a possible metabolic control mechanism. J. Biol. Chem. 238 (1963) 2875–2881. [PMID: 14063317]
2.  Kornberg, A. and Pricer, W.E. Di- and triphosphopyridine nucleotide isocitric dehydrogenase in yeast. J. Biol. Chem. 189 (1951) 123–136. [PMID: 14832224]
3.  Plaut, G.W.E. Isocitrate dehydrogenases. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), The Enzymes, 2nd edn, vol. 7, Academic Press, New York, 1963, pp. 105–126.
4.  Plaut, G.W.E. and Sung, S.-C. Diphosphopyridine nucleotide isocitric dehydrogenase from animal tissues. J. Biol. Chem. 207 (1954) 305–314. [PMID: 13152105]
5.  Ramakrishnan, C.V. and Martin, S.M. Isocitric dehydrogenase in Aspergillus niger. Arch. Biochem. Biophys. 55 (1955) 403–407.
6.  Vickery, H.B. A suggested new nomenclature for the isomers of isocitric acid. J. Biol. Chem. 237 (1962) 1739–1741. [PMID: 13925783]
7.  Camacho, M.L., Brown, R.A., Bonete, M.J., Danson, M.J. and Hough, D.W. Isocitrate dehydrogenases from Haloferax volcanii and Sulfolobus solfataricus: enzyme purification, characterisation and N-terminal sequence. FEMS Microbiol. Lett. 134 (1995) 85–90. [DOI] [PMID: 8593959]
8.  Kim, Y.O., Koh, H.J., Kim, S.H., Jo, S.H., Huh, J.W., Jeong, K.S., Lee, I.J., Song, B.J. and Huh, T.L. Identification and functional characterization of a novel, tissue-specific NAD+-dependent isocitrate dehydrogenase β subunit isoform. J. Biol. Chem. 274 (1999) 36866–36875. [DOI] [PMID: 10601238]
9.  Inoue, H., Tamura, T., Ehara, N., Nishito, A., Nakayama, Y., Maekawa, M., Imada, K., Tanaka, H. and Inagaki, K. Biochemical and molecular characterization of the NAD+-dependent isocitrate dehydrogenase from the chemolithotroph Acidithiobacillus thiooxidans. FEMS Microbiol. Lett. 214 (2002) 127–132. [DOI] [PMID: 12204383]
[EC 1.1.1.41 created 1961, modified 2005]
 
 
EC 1.1.1.42     
Accepted name: isocitrate dehydrogenase (NADP+)
Reaction: isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH + H+ (overall reaction)
(1a) isocitrate + NADP+ = oxalosuccinate + NADPH + H+
(1b) oxalosuccinate = 2-oxoglutarate + CO2
For diagram of the citric-acid cycle, click here
Glossary: isocitrate = (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate (previously known as threo-Ds-isocitrate)
oxalosuccinate = 1-oxopropane-1,2,3-tricarboxylate
Other name(s): oxalosuccinate decarboxylase; oxalsuccinic decarboxylase; isocitrate (NADP) dehydrogenase; isocitrate (nicotinamide adenine dinucleotide phosphate) dehydrogenase; NADP-specific isocitrate dehydrogenase; NADP-linked isocitrate dehydrogenase; NADP-dependent isocitrate dehydrogenase; NADP isocitric dehydrogenase; isocitrate dehydrogenase (NADP-dependent); NADP-dependent isocitric dehydrogenase; triphosphopyridine nucleotide-linked isocitrate dehydrogenase-oxalosuccinate carboxylase; NADP+-linked isocitrate dehydrogenase; IDH (ambiguous); dual-cofactor-specific isocitrate dehydrogenase; NADP+-ICDH; NADP+-IDH; IDP; IDP1; IDP2; IDP3
Systematic name: isocitrate:NADP+ oxidoreductase (decarboxylating)
Comments: Requires Mn2+ or Mg2+ for activity. Unlike EC 1.1.1.41, isocitrate dehydrogenase (NAD+), oxalosuccinate can be used as a substrate. In eukaryotes, isocitrate dehydrogenase exists in two forms: an NAD+-linked enzyme found only in mitochondria and displaying allosteric properties, and a non-allosteric, NADP+-linked enzyme that is found in both mitochondria and cytoplasm [6]. The enzyme from some species can also use NAD+ but much more slowly [6,7].
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9028-48-2
References:
1.  Agosin, M.U. and Weinbach, E.C. Partial purification and characterization of the isocitric dehydrogenase from Trypanosoma cruzi. Biochim. Biophys. Acta 21 (1956) 117–126. [DOI] [PMID: 13363868]
2.  Moyle, J. and Dixon, M. Purification of the isocitrate enzyme (triphosphopyridine nucleotide-linked isocitrate dehydrogenase-oxalosuccinate carboxylase). Biochem. J. 63 (1956) 548–552. [PMID: 13355848]
3.  Plaut, G.W.E. Isocitrate dehydrogenases. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), The Enzymes, 2nd edn, vol. 7, Academic Press, New York, 1963, pp. 105–126.
4.  Siebert, G., Dubuc, J., Warner, R.C. and Plaut, G.W.E. The preparation of isocitrate dehydrogenase from mammalian heart. J. Biol. Chem. 226 (1957) 965–975. [PMID: 13438885]
5.  Vickery, H.B. A suggested new nomenclature for the isomers of isocitric acid. J. Biol. Chem. 237 (1962) 1739–1741. [PMID: 13925783]
6.  Camacho, M.L., Brown, R.A., Bonete, M.J., Danson, M.J. and Hough, D.W. Isocitrate dehydrogenases from Haloferax volcanii and Sulfolobus solfataricus: enzyme purification, characterisation and N-terminal sequence. FEMS Microbiol. Lett. 134 (1995) 85–90. [DOI] [PMID: 8593959]
7.  Steen, I.H., Lien, T. and Birkeland, N.-K. Biochemical and phylogenetic characterization of isocitrate dehydrogenase from a hyperthermophilic archaeon, Archaeoglobus fulgidus. Arch. Microbiol. 168 (1997) 412–420. [PMID: 9325430]
8.  Koh, H.J., Lee, S.M., Son, B.G., Lee, S.H., Ryoo, Z.Y., Chang, K.T., Park, J.W., Park, D.C., Song, B.J., Veech, R.L., Song, H. and Huh, T.L. Cytosolic NADP+-dependent isocitrate dehydrogenase plays a key role in lipid metabolism. J. Biol. Chem. 279 (2004) 39968–39974. [DOI] [PMID: 15254034]
9.  Ceccarelli, C., Grodsky, N.B., Ariyaratne, N., Colman, R.F. and Bahnson, B.J. Crystal structure of porcine mitochondrial NADP+-dependent isocitrate dehydrogenase complexed with Mn2+ and isocitrate. Insights into the enzyme mechanism. J. Biol. Chem. 277 (2002) 43454–43462. [DOI] [PMID: 12207025]
[EC 1.1.1.42 created 1961, modified 2005]
 
 
EC 1.1.1.87     
Accepted name: homoisocitrate dehydrogenase
Reaction: (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD+ = 2-oxoadipate + CO2 + NADH + H+
For diagram of l-lysine synthesis, click here
Glossary: homoisocitrate = (-)-threo-homoisocitrate = (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate
Other name(s): 2-hydroxy-3-carboxyadipate dehydrogenase; 3-carboxy-2-hydroxyadipate dehydrogenase; homoisocitric dehydrogenase; (-)-1-hydroxy-1,2,4-butanetricarboxylate:NAD+ oxidoreductase (decarboxylating); 3-carboxy-2-hydroxyadipate:NAD+ oxidoreductase (decarboxylating); HICDH
Systematic name: (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate:NAD+ oxidoreductase (decarboxylating)
Comments: Forms part of the lysine biosynthesis pathway in fungi [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9067-90-7
References:
1.  Strassman, M. and Ceci, L.N. Enzymatic formation of α-ketoadipic acid from homoisocitric acid. J. Biol. Chem. 240 (1965) 4357–4361. [PMID: 4284830]
2.  Rowley, B. and Tucci, A.F. Homoisocitric dehydrogenase from yeast. Arch. Biochem. Biophys. 141 (1970) 499–510. [DOI] [PMID: 4395693]
3.  Zabriskie, T.M. and Jackson, M.D. Lysine biosynthesis and metabolism in fungi. Nat. Prod. Rep. 17 (2000) 85–97. [PMID: 10714900]
[EC 1.1.1.87 created 1972 (EC 1.1.1.155 created 1976, incorporated 2004)]
 
 
EC 1.1.1.155      
Deleted entry: homoisocitrate dehydrogenase. The enzyme is identical to EC 1.1.1.87, homoisocitrate dehydrogenase
[EC 1.1.1.155 created 1976, deleted 2004]
 
 
EC 1.1.1.286     
Accepted name: isocitrate—homoisocitrate dehydrogenase
Reaction: (1) isocitrate + NAD+ = 2-oxoglutarate + CO2 + NADH
(2) (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD+ = 2-oxoadipate + CO2 + NADH + H+
Glossary: isocitrate = (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate (previously known as threo-Ds-isocitrate)
homoisocitrate = (-)-threo-homoisocitrate = (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate
Other name(s): homoisocitrate—isocitrate dehydrogenase; PH1722
Systematic name: isocitrate(homoisocitrate):NAD+ oxidoreductase (decarboxylating)
Comments: Requires Mn2+ and K+ or NH4+ for activity. Unlike EC 1.1.1.41, isocitrate dehydrogenase (NAD+) and EC 1.1.1.87, homoisocitrate dehydrogenase, this enzyme, from Pyrococcus horikoshii, can use both isocitrate and homoisocitrate as substrates. The enzyme may play a role in both the lysine and glutamate biosynthesis pathways.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Miyazaki, K. Bifunctional isocitrate-homoisocitrate dehydrogenase: a missing link in the evolution of β-decarboxylating dehydrogenase. Biochem. Biophys. Res. Commun. 331 (2005) 341–346. [DOI] [PMID: 15845397]
[EC 1.1.1.286 created 2005]
 
 
EC 2.1.1.144     
Accepted name: trans-aconitate 2-methyltransferase
Reaction: S-adenosyl-L-methionine + trans-aconitate = S-adenosyl-L-homocysteine + (E)-3-(methoxycarbonyl)pent-2-enedioate
For diagram of reaction, click here
Glossary: trans-aconitate = (E)-prop-1-ene-1,2,3-tricarboxylate
Systematic name: S-adenosyl-L-methionine:(E)-prop-1-ene-1,2,3-tricarboxylate 2′-O-methyltransferase
Comments: Also catalyses the formation of the methyl monoester of cis-aconitate, isocitrate and citrate, but more slowly. While the enzyme from Escherichia coli forms (E)-3-(methoxycarbonyl)-pent-2-enedioate as the product, that from Saccharomyces cerevisiae forms (E)-2-(methoxycarbonylmethyl)butenedioate and is therefore classified as a separate enzyme (cf. EC 2.1.1.145, trans-aconitate 3-methyltransferase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 235107-12-7
References:
1.  Cai, H. and Clarke, S. A novel methyltransferase catalyzes the esterification of trans-aconitate in Escherichia coli. J. Biol. Chem. 274 (1999) 13470–13479. [DOI] [PMID: 10224113]
2.  Cai, H., Strouse, J., Dumlao, D., Jung, M.E. and Clarke, S. Distinct reactions catalyzed by bacterial and yeast trans-aconitate methyltransferase. Biochemistry 40 (2001) 2210–2219. [DOI] [PMID: 11329290]
3.  Cai, H., Dumlao, D., Katz, J.E. and Clarke, S. Identification of the gene and characterization of the activity of the trans-aconitate methyltransferase from Saccharomyces cerevisiae. Biochemistry 40 (2001) 13699–13709. [DOI] [PMID: 11695919]
[EC 2.1.1.144 created 2002]
 
 
EC 2.1.1.145     
Accepted name: trans-aconitate 3-methyltransferase
Reaction: S-adenosyl-L-methionine + trans-aconitate = S-adenosyl-L-homocysteine + (E)-2-(methoxycarbonylmethyl)butenedioate
For diagram of reaction, click here
Glossary: trans-aconitate = (E)-prop-1-ene-1,2,3-tricarboxylate
Systematic name: S-adenosyl-L-methionine:(E)-prop-1-ene-1,2,3-tricarboxylate 3′-O-methyltransferase
Comments: Also catalyses the formation of the methyl monoester of cis-aconitate, isocitrate and citrate, but more slowly. While the enzyme from Saccharomyces cerevisiae forms (E)-2-(methoxycarbonylmethyl)butenedioate as the product, that from Escherichia coli forms (E)-3-(methoxycarbonyl)-pent-2-enedioate and is therefore classified as a separate enzyme (cf. EC 2.1.1.144, trans-aconitate 2-methyltransferase)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 235107-12-7
References:
1.  Cai, H. and Clarke, S. A novel methyltransferase catalyzes the esterification of trans-aconitate in Escherichia coli. J. Biol. Chem. 274 (1999) 13470–13479. [DOI] [PMID: 10224113]
2.  Cai, H., Strouse, J., Dumlao, D., Jung, M.E. and Clarke, S. Distinct reactions catalyzed by bacterial and yeast trans-aconitate methyltransferase. Biochemistry 40 (2001) 2210–2219. [DOI] [PMID: 11329290]
[EC 2.1.1.145 created 2002]
 
 
EC 2.3.1.126     
Accepted name: isocitrate O-dihydroxycinnamoyltransferase
Reaction: caffeoyl-CoA + isocitrate = CoA + 2-O-caffeoylisocitrate
Glossary: 2-O-caffeoylisocitrate = (1R,2S)-1-{[3-(E)-(3,4-dihydroxyphenyl)acryloyl]oxy}propane-1,2,3-tricarboxylate = (3S,4R)-3-carboxy-2,3-dideoxy-4-O-[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]pentarate
isocitrate = (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate = threo-Ds-isocitrate
Systematic name: caffeoyl-CoA:isocitrate 2-O-(3,4-dihydroxycinnamoyl)transferase
Comments: Feruloyl-CoA and 4-coumaroyl-CoA can also act as donors.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 112352-88-2
References:
1.  Strack, D., Leicht, P., Bokern, M., Wray, V. and Grotjahn, L. Hydroxycinnamic acid-esters of isocitric acid - accumulation and enzymatic-synthesis in Amaranthus cruentus. Phytochemistry 26 (1987) 2919–2922.
[EC 2.3.1.126 created 1990]
 
 
EC 2.7.1.37      
Transferred entry: protein kinase. Now divided into EC 2.7.11.1 (non-specific serine/threonine protein kinase), EC 2.7.11.8 (Fas-activated serine/threonine kinase), EC 2.7.11.9 (Goodpasture-antigen-binding protein kinase), EC 2.7.11.10 (IκB kinase), EC 2.7.11.11 (cAMP-dependent protein kinase), EC 2.7.11.12 (cGMP-dependent protein kinase), EC 2.7.11.13 (protein kinase C), EC 2.7.11.21 (polo kinase), EC 2.7.11.22 (cyclin-dependent kinase), EC 2.7.11.24 (mitogen-activated protein kinase), EC 2.7.11.25 (mitogen-activated protein kinase kinase kinase), EC 2.7.11.30 (receptor protein serine/threonine kinase) and EC 2.7.12.1 (dual-specificity kinase)
[EC 2.7.1.37 created 1961 (EC 2.7.1.70 incorporated 2004), deleted 2005]
 
 
EC 2.7.1.116      
Transferred entry: [isocitrate dehydrogenase (NADP+)] kinase. Now EC 2.7.11.5, [isocitrate dehydrogenase (NADP+)] kinase
[EC 2.7.1.116 created 1986, deleted 2005]
 
 
EC 2.7.11.5     
Accepted name: [isocitrate dehydrogenase (NADP+)] kinase
Reaction: ATP + [isocitrate dehydrogenase (NADP+)] = ADP + [isocitrate dehydrogenase (NADP+)] phosphate
Other name(s): [isocitrate dehydrogenase (NADP)] kinase; ICDH kinase/phosphatase; IDH kinase; IDH kinase/phosphatase; IDH-K/P; IDHK/P; isocitrate dehydrogenase kinase (phosphorylating); isocitrate dehydrogenase kinase/phosphatase; STK3
Systematic name: ATP:[isocitrate dehydrogenase (NADP+)] phosphotransferase
Comments: The enzyme has no activating compound but is specific for its substrate. Phosphorylates and inactivates EC 1.1.1.42, isocitrate dehydrogenase (NADP+).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 83682-93-3
References:
1.  Wang, J.Y.J. and Koshland, D.E., Jr. The reversible phosphorylation of isocitrate dehydrogenase of Salmonella typhimurium. Arch. Biochem. Biophys. 218 (1982) 59–67. [DOI] [PMID: 6756316]
2.  Miller, S.P., Karschnia, E.J., Ikeda, T.P. and LaPorte, D.C. Isocitrate dehydrogenase kinase/phosphatase. Kinetic characteristics of the wild-type and two mutant proteins. J. Biol. Chem. 271 (1996) 19124–19128. [DOI] [PMID: 8702587]
3.  Singh, S.K., Matsuno, K., LaPorte, D.C. and Banaszak, L.J. Crystal structure of Bacillus subtilis isocitrate dehydrogenase at 1.55 Å. Insights into the nature of substrate specificity exhibited by Escherichia coli isocitrate dehydrogenase kinase/phosphatase. J. Biol. Chem. 276 (2001) 26154–26163. [DOI] [PMID: 11290745]
4.  Oudot, C., Cortay, J.C., Blanchet, C., Laporte, D.C., Di Pietro, A., Cozzone, A.J. and Jault, J.M. The "catalytic" triad of isocitrate dehydrogenase kinase/phosphatase from E. coli and its relationship with that found in eukaryotic protein kinases. Biochemistry 40 (2001) 3047–3055. [DOI] [PMID: 11258918]
[EC 2.7.11.5 created 1986 as EC 2.7.1.116, transferred 2005 to EC 2.7.11.5]
 
 
EC 3.11.1.3     
Accepted name: phosphonopyruvate hydrolase
Reaction: 3-phosphonopyruvate + H2O = pyruvate + phosphate
For diagram of phosphonate metabolism, click here
Other name(s): PPH
Comments: Highly specific for phosphonopyruvate as substrate [2]. The reaction is not inhibited by phosphate but is inhibited by the phosphonates phosphonoformic acid, hydroxymethylphosphonic acid and 3-phosphonopropanoic acid [2]. The enzyme is activated by the divalent cations Co2+, Mg2+ and Mn2+. This enzyme is a member of the phosphoenolpyruvate mutase/isocitrate lyase superfamily [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Ternan, N.G., Hamilton, J.T. and Quinn, J.P. Initial in vitro characterisation of phosphonopyruvate hydrolase, a novel phosphate starvation-independent, carbon-phosphorus bond cleavage enzyme in Burkholderia cepacia Pal6. Arch. Microbiol. 173 (2000) 35–41. [PMID: 10648102]
2.  Kulakova, A.N., Wisdom, G.B., Kulakov, L.A. and Quinn, J.P. The purification and characterization of phosphonopyruvate hydrolase, a novel carbon-phosphorus bond cleavage enzyme from Variovorax sp. Pal2. J. Biol. Chem. 278 (2003) 23426–23431. [DOI] [PMID: 12697754]
3.  Chen, C.C., Han, Y., Niu, W., Kulakova, A.N., Howard, A., Quinn, J.P., Dunaway-Mariano, D. and Herzberg, O. Structure and kinetics of phosphonopyruvate hydrolase from Variovorax sp. Pal2: new insight into the divergence of catalysis within the PEP mutase/isocitrate lyase superfamily. Biochemistry 45 (2006) 11491–11504. [DOI] [PMID: 16981709]
[EC 3.11.1.3 created 2007]
 
 
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.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9024-98-0
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 4.1.3.1     
Accepted name: isocitrate lyase
Reaction: isocitrate = succinate + glyoxylate
For diagram of the glyoxylate cycle, click here
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].
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9045-78-7
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. [DOI] [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 4.1.3.24     
Accepted name: malyl-CoA lyase
Reaction: (1) (S)-malyl-CoA = acetyl-CoA + glyoxylate
(2) (2R,3S)-2-methylmalyl-CoA = propanoyl-CoA + glyoxylate
For diagram of the 3-hydroxypropanoate cycle, click here
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].
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 37290-67-8
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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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) . [DOI] [PMID: 27920298]
[EC 4.1.3.24 created 1972, modified 2014]
 
 
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.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 57827-77-7
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 4.2.1.3     
Accepted name: aconitate hydratase
Reaction: citrate = isocitrate (overall reaction)
(1a) citrate = cis-aconitate + H2O
(1b) cis-aconitate + H2O = isocitrate
For diagram of the citric acid cycle, click here and for diagram of the glyoxylate cycle, click here
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.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9024-25-3
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. [DOI] [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 4.2.1.36     
Accepted name: homoaconitate hydratase
Reaction: (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate = (Z)-but-1-ene-1,2,4-tricarboxylate + H2O
For diagram of l-lysine synthesis, click here
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].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9030-68-6
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. [DOI] [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 4.2.1.79     
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].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 80891-26-5
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. [DOI] [PMID: 12473114]
[EC 4.2.1.79 created 1984]
 
 
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.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 170780-51-5
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 4.2.1.114     
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
For diagram of the 2-aminoadipate pathway of L-lysine synthesis, click here
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 dihomoaconitate and trihomoaconitate as well as the non-physiological substrate tetrahomoaconitate. cis-Aconitate and threo-DL-isocitrate cannot act as substrates, and (S)-homocitrate and trans-homoaconitate act as inhibitors of the enzyme.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
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. [DOI] [PMID: 18765671]
[EC 4.2.1.114 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.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
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. [DOI] [PMID: 14702315]
[EC 4.2.1.117 created 2009]
 
 
EC 5.1.2.6     
Accepted name: isocitrate epimerase
Reaction: (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate = (1S,2S)-1-hydroxypropane-1,2,3-tricarboxylate
For diagram of reaction, click here
Glossary: isocitrate = (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate = threo-Ds-isocitrate
allocitrate = (1S,2S)-1-hydroxypropane-1,2,3-tricarboxylate = D-erythro-isocitrate
Systematic name: (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate 1-epimerase
Comments: (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate is the commonly occurring isomer of isocitrate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 81210-68-6
References:
1.  Hoshiko, S., Kunimoto, Y., Arima, K. and Beppu, T. Mechanism of L-alloisocitric acid fermentation: isocitrate epimerase activity in the cell-free-extract of Penicillium purpurogenum. Agric. Biol. Chem. 46 (1982) 143–151.
[EC 5.1.2.6 created 1984]
 
 
EC 6.4.1.7     
Accepted name: 2-oxoglutarate carboxylase
Reaction: ATP + 2-oxoglutarate + HCO3- = ADP + phosphate + oxalosuccinate
For diagram of reaction, click here
Glossary: oxalosuccinate = 1-oxopropane-1,2,3-tricarboxylate
Other name(s): oxalosuccinate synthetase; carboxylating factor for ICDH (incorrect); CFI; OGC
Comments: A biotin-containing enzyme that requires Mg2+ for activity. It was originally thought [1] that this enzyme was a promoting factor for the carboxylation of 2-oxoglutarate by EC 1.1.1.41, isocitrate dehydrogenase (NAD+), but this has since been disproved [2]. The product of the reaction is unstable and is quickly converted into isocitrate by the action of EC 1.1.1.41 [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 60382-75-4
References:
1.  Aoshima, M., Ishii, M. and Igarashi, Y. A novel biotin protein required for reductive carboxylation of 2-oxoglutarate by isocitrate dehydrogenase in Hydrogenobacter thermophilus TK-6. Mol. Microbiol. 51 (2004) 791–798. [DOI] [PMID: 14731279]
2.  Aoshima, M. and Igarashi, Y. A novel oxalosuccinate-forming enzyme involved in the reductive carboxylation of 2-oxoglutarate in Hydrogenobacter thermophilus TK-6. Mol. Microbiol. 62 (2006) 748–759. [DOI] [PMID: 17076668]
[EC 6.4.1.7 created 2006]
 
 


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