The Enzyme Database

Displaying entries 151-200 of 339.

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EC 5.3.3.8     
Accepted name: Δ3-Δ2-enoyl-CoA isomerase
Reaction: (1) a (3Z)-alk-3-enoyl-CoA = a (2E)-alk-2-enoyl-CoA
(2) a (3E)-alk-3-enoyl-CoA = a (2E)-alk-2-enoyl-CoA
For diagram of Benzoyl-CoA catabolism, click here
Other name(s): ECI (gene name); dodecenoyl-CoA isomerase; dodecenoyl-CoA Δ-isomerase; Δ3-cis-Δ2-trans-enoyl-CoA isomerase; acetylene-allene isomerase; dodecenoyl-CoA Δ3-cis-Δ2-trans-isomerase; dodecenoyl-CoA (3Z)-(2E)-isomerase
Systematic name: (3Z/3E)-alk-3-enoyl-CoA (2E)-isomerase
Comments: The enzyme participates in the β-oxidation of fatty acids with double bonds at an odd position. Processing of these substrates via the β-oxidation system results in intermediates with a cis- or trans-double bond at position C3, which cannot be processed further by the regular enzymes of the β-oxidation system. This enzyme isomerizes the bond to a trans bond at position C2, which can be processed further. The reaction rate is ten times higher for the (3Z) isomers than for (3E) isomers. The enzyme can also catalyse the isomerization of 3-acetylenic fatty acyl thioesters to 2,3-dienoyl fatty acyl thioesters.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 62213-29-0
References:
1.  Stoffel, W., Ditzer, R. and Caesar, H. Der Stoffwechsel der ungesättigten Fettsäuren. III. Zur β-Oxydation der Mono- und Polyenfettsäuren. Der Mechanismus der enzymatischen Reaktionen an Δ3cis-Enoyl-CoA-Verbindungen. Hoppe-Seyler's Z. Physiol. Chem. 339 (1964) 167–181. [PMID: 5830064]
2.  Stoffel, W. and Ecker, W. Δ3-cis,-Δ2-trans-Enoyl-CoA isomerase from rat liver mitochondria. Methods Enzymol. 14 (1969) 99–105.
3.  Stoffel, W. and Grol, M. Purification and properties of 3-cis-2-trans-enoyl-CoA isomerase (dodecenoyl-CoA Δ-isomerase) from rat liver mitochondria. Hoppe-Seyler's Z. Physiol. Chem. 359 (1978) 1777–1782. [PMID: 738702]
4.  Miesowicz, F.M. and Bloch, K. Purification of hog liver isomerase. Mechanism of isomerization of 3-alkenyl and 3-alkynyl thioesters. J. Biol. Chem. 254 (1979) 5868–5877. [PMID: 376522]
5.  Engeland, K. and Kindl, H. Purification and characterization of a plant peroxisomal Δ2,Δ3-enoyl-CoA isomerase acting on 3-cis-enoyl-CoA and 3-trans-enoyl-CoA. Eur. J. Biochem. 196 (1991) 699–705. [DOI] [PMID: 2013292]
6.  Geisbrecht, B.V., Zhang, D., Schulz, H. and Gould, S.J. Characterization of PECI, a novel monofunctional Δ3, Δ2-enoyl-CoA isomerase of mammalian peroxisomes. J. Biol. Chem. 274 (1999) 21797–21803. [DOI] [PMID: 10419495]
7.  Zhang, D., Yu, W., Geisbrecht, B.V., Gould, S.J., Sprecher, H. and Schulz, H. Functional characterization of Δ3,Δ2-enoyl-CoA isomerases from rat liver. J. Biol. Chem. 277 (2002) 9127–9132. [DOI] [PMID: 11781327]
8.  Goepfert, S., Vidoudez, C., Tellgren-Roth, C., Delessert, S., Hiltunen, J.K. and Poirier, Y. Peroxisomal Δ3,Δ2-enoyl CoA isomerases and evolution of cytosolic paralogues in embryophytes. Plant J. 56 (2008) 728–742. [DOI] [PMID: 18657232]
[EC 5.3.3.8 created 1978, modified 1980, modified 2018]
 
 
EC 5.3.3.9     
Accepted name: prostaglandin-A1 Δ-isomerase
Reaction: (13E)-(15S)-15-hydroxy-9-oxoprosta-10,13-dienoate = (13E)-(15S)-15-hydroxy-9-oxoprosta-11,13-dienoate
Other name(s): prostaglandin A isomerase
Systematic name: (13E)-(15S)-15-hydroxy-9-oxoprosta-10,13-dienoate Δ10-Δ11-isomerase
Comments: Interconverts prostaglandin A1 and prostaglandin C1.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9055-01-0
References:
1.  Polet, H. and Levine, L. Metabolism of prostaglandins E, A and C in serum. J. Biol. Chem. 250 (1975) 351–357. [PMID: 234423]
[EC 5.3.3.9 created 1978]
 
 
EC 5.3.3.10     
Accepted name: 5-carboxymethyl-2-hydroxymuconate Δ-isomerase
Reaction: 5-carboxymethyl-2-hydroxymuconate = (3E,5R)-5-carboxy-2-oxohept-3-enedioate
Glossary: 5-carboxymethyl-2-hydroxymuconate = (2E,4Z)-5-hydroxypenta-2,4-diene-1,2,5-tricarboxylate
Other name(s): CHM isomerase; 5-carboxymethyl-2-hydroxymuconic acid isomerase
Systematic name: 5-carboxymethyl-2-hydroxymuconate Δ2,Δ4-2-oxo,Δ3-isomerase
Comments: Part of the homoprotocatechuate degradation pathway in Escherichia coli C.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 79079-05-3
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. [DOI] [PMID: 7026235]
2.  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 5.3.3.10 created 1984]
 
 
EC 5.3.3.11     
Accepted name: isopiperitenone Δ-isomerase
Reaction: isopiperitenone = piperitenone
For diagram of (–)-carvone, perillyl aldehyde and pulegone biosynthesis, click here
Systematic name: isopiperitenone Δ8-Δ4-isomerase
Comments: Involved in the biosynthesis of menthol and related monoterpenes in peppermint (Mentha piperita) leaves.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 96595-07-2
References:
1.  Kjonaas, R.B., Venkatachalam, K.V. and Croteau, R. Metabolism of monoterpenes: oxidation of isopiperitenol to isopiperitenone, and subsequent isomerization to piperitenone by soluble enzyme preparations from peppermint (Mentha piperita) leaves. Arch. Biochem. Biophys. 238 (1985) 49–60. [DOI] [PMID: 3885858]
[EC 5.3.3.11 created 1989]
 
 
EC 5.3.3.12     
Accepted name: L-dopachrome isomerase
Reaction: L-dopachrome = 5,6-dihydroxyindole-2-carboxylate
For diagram of melanin biosynthesis, click here
Glossary: L-dopachrome = (2S)-5,6-dioxo-2,3,5,6-tetrahydro-1H-indole-2-carboxylate
Other name(s): dopachrome tautomerase; tyrosinase-related protein 2; TRP-1; TRP2; TRP-2; tyrosinase-related protein-2; dopachrome Δ7,Δ2-isomerase; dopachrome Δ-isomerase; dopachrome conversion factor; dopachrome isomerase; dopachrome oxidoreductase; dopachrome-rearranging enzyme; DCF; DCT; dopachrome keto-enol isomerase; L-dopachrome-methyl ester tautomerase
Systematic name: L-dopachrome keto-enol isomerase
Comments: A zinc enzyme. Stereospecific for L-dopachrome. Dopachrome methyl ester is a substrate, but dopaminochrome (2,3-dihydroindole-5,6-quinone) is not (see also EC 4.1.1.84, D-dopachrome decarboxylase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 130122-81-5
References:
1.  Solano, F., Jiménez-Cervantes, C., Martinez-Liarte, J.H., Garcia-Borrón, J.C. and Lozano, J.A. Molecular mechanism for catalysis by a new zinc enzyme, dopachrome tautomerase. Biochem. J. 313 (1996) 447–453. [PMID: 8573077]
2.  Pawelek, J.M. Dopachrome conversion factor functions as an isomerase. Biochem. Biophys. Res. Commun. 166 (1990) 1328–1333. [DOI] [PMID: 2106316]
3.  Pennock, J.L., Behnke, J.M., Bickle, Q.D., Devaney, E., Grencis, R.K., Isaac, R.E. , Joshua. G.W., Selkirk. M.E., Zhang. Y. and Meyer, D.J. Rapid purification and characterization of L-dopachrome-methyl ester tautomerase (macrophage-migration-inhibitory factor) from Trichinella spiralis, Trichuris muris and Brugia pahangi. Biochem. J. 335 (1998) 495–498. [PMID: 9794786]
[EC 5.3.3.12 created 1992, modified 1999, modified 2005]
 
 
EC 5.3.3.13     
Accepted name: polyenoic fatty acid isomerase
Reaction: (5Z,8Z,11Z,14Z,17Z)-icosapentaenoate = (5Z,7E,9E,14Z,17Z)-icosapentaenoate
For diagram of reaction, click here
Other name(s): PFI; eicosapentaenoate cis-Δ5,8,11,14,17-eicosapentaenoate cis-Δ5-trans-Δ7,9-cis-Δ14,17 isomerase; (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate Δ8,11-Δ7,8-isomerase (incorrect); (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate Δ8,11-Δ7,9-isomerase (trans-double-bond-forming)
Systematic name: (5Z,8Z,11Z,14Z,17Z)-icosapentaenoate Δ8,11-Δ7,9-isomerase (trans-double-bond-forming)
Comments: The enzyme from the red alga Ptilota filicina catalyses the isomerization of skip dienes (methylene-interrupted double bonds) in a broad range of fatty acids and fatty-acid analogues, such as arachidonate and γ-linolenate, to yield a conjugated triene.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 159002-84-3
References:
1.  Wise, M.L., Hamberg, M. and Gerwick, W.H. Biosynthesis of conjugated fatty acids by a novel isomerase from the red marine alga Ptilota filicina. Biochemistry 33 (1994) 15223–15232. [PMID: 7803384]
2.  Wise, M.L., Soderstrom, K., Murray, T.F. and Gerwick, W.H. Synthesis and cannabinoid receptor binding activity of conjugated triene anandamide, a novel eicosanoid. Experientia 52 (1996) 88–92. [PMID: 8575565]
3.  Wise, M.L., Rossi, J. and Gerwick, W.H. Binding site characterization of polyenoic fatty-acid isomerase from the marine alga Ptilota filicina. Biochemistry 36 (1997) 2985–2992. [DOI] [PMID: 9062129]
4.  Zheng, W., Wise, M.L., Wyrick, A., Metz, J.G., Yuan, L. and Gerwick, W.H. Polyenoic fatty-acid isomerase from the marine red alga Ptilota filicina: protein characterization and functional expression of the cloned cDNA. Arch. Biochem. Biophys. 401 (2002) 11–20. [DOI] [PMID: 12054482]
[EC 5.3.3.13 created 2004]
 
 
EC 5.3.3.14     
Accepted name: trans-2-decenoyl-[acyl-carrier protein] isomerase
Reaction: a trans-dec-2-enoyl-[acyl-carrier protein] = a cis-dec-3-enoyl-[acyl-carrier protein]
Other name(s): β-hydroxydecanoyl thioester dehydrase; trans-2-cis-3-decenoyl-ACP isomerase; trans-2,cis-3-decenoyl-ACP isomerase; trans-2-decenoyl-ACP isomerase; FabM; decenoyl-[acyl-carrier-protein] Δ2-trans-Δ3-cis-isomerase
Systematic name: decenoyl-[acyl-carrier protein] Δ2-trans-Δ3-cis-isomerase
Comments: While the enzyme from Escherichia coli is highly specific for the 10-carbon enoyl-ACP, the enzyme from Streptococcus pneumoniae can also use the 12-carbon enoyl-ACP as substrate in vitro but not 14- or 16-carbon enoyl-ACPs [3]. ACP can be replaced by either CoA or N-acetylcysteamine thioesters. The cis-3-enoyl product is required to form unsaturated fatty acids, such as palmitoleic acid and cis-vaccenic acid, in dissociated (or type II) fatty-acid biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9030-80-2
References:
1.  Brock, D.J.H., Kass, L.R. and Bloch, K. β-Hydroxydecanoyl thioester dehydrase. II. Mode of action. J. Biol. Chem. 242 (1967) 4432–4440. [PMID: 4863740]
2.  Bloch, K. Enzymatic synthesis of monounsaturated fatty acids. Acc. Chem. Res. 2 (1969) 193–202.
3.  Marrakchi, H., Choi, K.H. and Rock, C.O. A new mechanism for anaerobic unsaturated fatty acid formation in Streptococcus pneumoniae. J. Biol. Chem. 277 (2002) 44809–44816. [DOI] [PMID: 12237320]
4.  Cronan, J.E., Jr. and Rock, C.O. Biosynthesis of membrane lipids. In: Neidhardt, F.C. (Ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd edn, vol. 1, ASM Press, Washington, DC, 1996, pp. 612–636.
[EC 5.3.3.14 created 2006]
 
 
EC 5.3.3.15      
Transferred entry: ascopyrone tautomerase. Now EC 5.3.2.7, ascopyrone tautomerase
[EC 5.3.3.15 created 2006, deleted 2013]
 
 
EC 5.3.3.16      
Transferred entry: 4-oxalomesaconate tautomerase. Now EC 5.3.2.8, 4-oxalomesaconate tautomerase
[EC 5.3.3.16 created 2011, modified 2011, deleted 2013]
 
 
EC 5.3.3.17     
Accepted name: trans-2,3-dihydro-3-hydroxyanthranilate isomerase
Reaction: (5S,6S)-6-amino-5-hydroxycyclohexa-1,3-diene-1-carboxyate = (1R,6S)-6-amino-5-oxocyclohex-2-ene-1-carboxylate
For diagram of enediyne antitumour antibiotic biosynthesis and pyocyanin biosynthesis, click here
Glossary: (5S,6S)-6-amino-5-hydroxycyclohexa-1,3-diene-1-carboxylate = trans-2,3-dihydro-3-hydroxyanthranilate
Other name(s): phzF (gene name); (5S,6S)-6-amino-5-hydroxycyclohexane-1,3-diene-1-carboxyate isomerase (incorrect)
Systematic name: (5S,6S)-6-amino-5-hydroxycyclohexa-1,3-diene-1-carboxyate isomerase
Comments: The enzyme is involved in phenazine biosynthesis. The product probably spontaneously dimerises to 1,4,5a,6,9,10a-hexahydrophenazine-1,6-dicarboxylate
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Parsons, J.F., Song, F., Parsons, L., Calabrese, K., Eisenstein, E. and Ladner, J.E. Structure and function of the phenazine biosynthesis protein PhzF from Pseudomonas fluorescens 2-79. Biochemistry 43 (2004) 12427–12435. [DOI] [PMID: 15449932]
2.  Blankenfeldt, W., Kuzin, A.P., Skarina, T., Korniyenko, Y., Tong, L., Bayer, P., Janning, P., Thomashow, L.S. and Mavrodi, D.V. Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens. Proc. Natl. Acad. Sci. USA 101 (2004) 16431–16436. [DOI] [PMID: 15545603]
3.  Parsons, J.F., Calabrese, K., Eisenstein, E. and Ladner, J.E. Structure of the phenazine biosynthesis enzyme PhzG. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 2110–2113. [DOI] [PMID: 15502343]
4.  Mavrodi, D.V., Bleimling, N., Thomashow, L.S. and Blankenfeldt, W. The purification, crystallization and preliminary structural characterization of PhzF, a key enzyme in the phenazine-biosynthesis pathway from Pseudomonas fluorescens 2-79. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 184–186. [PMID: 14684924]
5.  Ahuja, E.G., Janning, P., Mentel, M., Graebsch, A., Breinbauer, R., Hiller, W., Costisella, B., Thomashow, L.S., Mavrodi, D.V. and Blankenfeldt, W. PhzA/B catalyzes the formation of the tricycle in phenazine biosynthesis. J. Am. Chem. Soc. 130 (2008) 17053–17061. [DOI] [PMID: 19053436]
[EC 5.3.3.17 created 2011]
 
 
EC 5.3.3.18     
Accepted name: 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase
Reaction: 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA = 2-oxepin-2(3H)-ylideneacetyl-CoA
For diagram of aerobic phenylacetate catabolism, click here
Glossary: 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA = 2-{7-oxabicyclo[4.1.0]hepta-2,4-dien-1-yl}acetyl-CoA
oxepin-CoA = 2-oxepin-2(3H)-ylideneacetyl-CoA
Other name(s): paaG (gene name); 1,2-epoxyphenylacetyl-CoA isomerase (misleading)
Systematic name: 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase
Comments: The enzyme catalyses the reversible isomerization of 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA to the unusual unsaturated, oxygen-containing, seven-member heterocyclic enol ether 2-oxepin-2(3H)-ylideneacetyl-CoA, as part of an aerobic phenylacetate degradation pathway.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Ismail, W., El-Said Mohamed, M., Wanner, B.L., Datsenko, K.A., Eisenreich, W., Rohdich, F., Bacher, A. and Fuchs, G. Functional genomics by NMR spectroscopy. Phenylacetate catabolism in Escherichia coli. Eur. J. Biochem. 270 (2003) 3047–3054. [DOI] [PMID: 12846838]
2.  Teufel, R., Mascaraque, V., Ismail, W., Voss, M., Perera, J., Eisenreich, W., Haehnel, W. and Fuchs, G. Bacterial phenylalanine and phenylacetate catabolic pathway revealed. Proc. Natl. Acad. Sci. USA 107 (2010) 14390–14395. [DOI] [PMID: 20660314]
[EC 5.3.3.18 created 2011]
 
 
EC 5.3.3.19     
Accepted name: 3-[(4R)-4-hydroxycyclohexa-1,5-dien-1-yl]-2-oxopropanoate isomerase
Reaction: 3-[(4R)-4-hydroxycyclohexa-1,5-dien-1-yl]-2-oxopropanoate = 3-[(1E,4R)-4-hydroxycyclohex-2-en-1-ylidene]-2-oxopropanoate
For diagram of bacilysin biosynthesis, click here
Glossary: L-anticapsin = 3-[(1R,2S,6R)-5-oxo-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine
Other name(s): BacB
Systematic name: 3-[(4R)-4-hydroxycyclohexa-1,5-dien-1-yl]-2-oxopropanoate isomerase
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 can interconvert the (E) isomer formed in the reaction into the (Z) isomer [2], although this isomerization is not part of the pathway leading to bacilysin [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
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. [DOI] [PMID: 20052993]
2.  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. [DOI] [PMID: 22483065]
3.  Parker, J.B. and Walsh, C.T. Action and timing of BacC and BacD in the late stages of biosynthesis of the dipeptide antibiotic bacilysin. Biochemistry 52 (2013) 889–901. [DOI] [PMID: 23317005]
[EC 5.3.3.19 created 2015]
 
 
EC 5.3.3.20      
Transferred entry: 2-hydroxyisobutanoyl-CoA mutase. Now EC 5.4.99.64, 2-hydroxyisobutanoyl-CoA mutase
[EC 5.3.3.20 created 2016, deleted 2017]
 
 
EC 5.3.3.21     
Accepted name: Δ3,5-Δ2,4-dienoyl-CoA isomerase
Reaction: a (3E,5Z)-alka-3,5-dienoyl-CoA = a (2E,4E)-alka-2,4-dienoyl-CoA
Other name(s): 3,5-tetradecadienoyl-CoA isomerase; DCI1 (gene name)
Systematic name: (3E,5Z)-alka-3,5-dienoyl-CoA Δ3,5-Δ2,4 isomerase
Comments: The enzyme participates in an alternative degradation route of fatty acids with cis-double bonds on odd-number carbons such as oleate and linoleate. The main physiological substrate is (3E,5Z)-tetradeca-3,5-dienoyl-CoA, but other (3E,5Z)-dienoyl-CoAs with varying carbon chain lengths are also substrates.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Filppula, S.A., Yagi, A.I., Kilpelainen, S.H., Novikov, D., FitzPatrick, D.R., Vihinen, M., Valle, D. and Hiltunen, J.K. Δ3,5-Δ2,4-dienoyl-CoA isomerase from rat liver. Molecular characterization. J. Biol. Chem. 273 (1998) 349–355. [DOI] [PMID: 9417087]
2.  Modis, Y., Filppula, S.A., Novikov, D.K., Norledge, B., Hiltunen, J.K. and Wierenga, R.K. The crystal structure of dienoyl-CoA isomerase at 1.5 Å resolution reveals the importance of aspartate and glutamate sidechains for catalysis. Structure 6 (1998) 957–970. [DOI] [PMID: 9739087]
3.  Geisbrecht, B.V., Schulz, K., Nau, K., Geraghty, M.T., Schulz, H., Erdmann, R. and Gould, S.J. Preliminary characterization of Yor180Cp: identification of a novel peroxisomal protein of saccharomyces cerevisiae involved in fatty acid metabolism. Biochem. Biophys. Res. Commun. 260 (1999) 28–34. [DOI] [PMID: 10381339]
4.  Gurvitz, A., Mursula, A.M., Yagi, A.I., Hartig, A., Ruis, H., Rottensteiner, H. and Hiltunen, J.K. Alternatives to the isomerase-dependent pathway for the β-oxidation of oleic acid are dispensable in Saccharomyces cerevisiae. Identification of YOR180c/DCI1 encoding peroxisomal Δ(3,5)-Δ(2,4)-dienoyl-CoA isomerase. J. Biol. Chem. 274 (1999) 24514–24521. [DOI] [PMID: 10455114]
5.  Zhang, D., Liang, X., He, X.Y., Alipui, O.D., Yang, S.Y. and Schulz, H. Δ3,5,Δ2,4-dienoyl-CoA isomerase is a multifunctional isomerase. A structural and mechanistic study. J. Biol. Chem. 276 (2001) 13622–13627. [DOI] [PMID: 11278886]
6.  Goepfert, S., Vidoudez, C., Rezzonico, E., Hiltunen, J.K. and Poirier, Y. Molecular identification and characterization of the Arabidopsis Δ3,5,Δ2,4-dienoyl-coenzyme A isomerase, a peroxisomal enzyme participating in the β-oxidation cycle of unsaturated fatty acids. Plant Physiol. 138 (2005) 1947–1956. [DOI] [PMID: 16040662]
[EC 5.3.3.21 created 2018]
 
 
EC 5.3.3.22     
Accepted name: lutein isomerase
Reaction: lutein = meso-zeaxanthin
For diagram of lutein biosynthesis, click here
Glossary: lutein = (3R,3′R)-dihydroxy-α-carotene
meso-zeaxanthin = (3R,3′S)-β,β-carotene-3,3′-diol
Other name(s): RPE65 (gene name); meso-zeaxanthin isomerase
Systematic name: lutein Δ4-Δ5-isomerase
Comments: The enzyme is found in the retinal pigment epithelium (RPE) of vertebrates. It also has the activity of EC 3.1.1.64, retinoid isomerohydrolase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Shyam, R., Gorusupudi, A., Nelson, K., Horvath, M.P. and Bernstein, P.S. RPE65 has an additional function as the lutein to meso-zeaxanthin isomerase in the vertebrate eye. Proc. Natl. Acad. Sci. USA 114 (2017) 10882–10887. [DOI] [PMID: 28874556]
[EC 5.3.3.22 created 2018]
 
 
EC 5.3.3.23     
Accepted name: S-methyl-5-thioribulose 1-phosphate isomerase
Reaction: (1) S-methyl-5-thio-D-ribulose 1-phosphate = S-methyl-1-thio-D-xylulose 5-phosphate
(2) S-methyl-5-thio-D-ribulose 1-phosphate = S-methyl-1-thio-D-ribulose 5-phosphate
Other name(s): rlp (gene name); 5-methylthioribulose-1-phosphate isomerase (incorrect)
Systematic name: S-methyl-5-thio-D-ribulose 1-phosphate 1,3-isomerase
Comments: The enzyme, characterized from the bacterium Rhodospirillum rubrum, participates in methionine salvage from S-methyl-5′-thioadenosine. It is a RuBisCO-like protein (RLP) that is not capable of carbon fixation, and catalyses an isomerization reaction that converts S-methyl-5-thio-D-ribulose 1-phosphate to a 3:1 mixture of S-methyl-1-thioxylulose 5-phosphate and S-methyl-1-thioribulose 5-phosphate. The reaction is an overall 1,3-proton transfer, which likely consists of two 1,2-proton transfer events.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Imker, H.J., Singh, J., Warlick, B.P., Tabita, F.R. and Gerlt, J.A. Mechanistic diversity in the RuBisCO superfamily: a novel isomerization reaction catalyzed by the RuBisCO-like protein from Rhodospirillum rubrum. Biochemistry 47 (2008) 11171–11173. [DOI] [PMID: 18826254]
2.  Erb, T.J., Evans, B.S., Cho, K., Warlick, B.P., Sriram, J., Wood, B.M., Imker, H.J., Sweedler, J.V., Tabita, F.R. and Gerlt, J.A. A RubisCO-like protein links SAM metabolism with isoprenoid biosynthesis. Nat. Chem. Biol. 8 (2012) 926–932. [DOI] [PMID: 23042035]
[EC 5.3.3.23 created 2021]
 
 
EC 5.3.3.24     
Accepted name: neopinone isomerase
Reaction: neopinone = codeinone
Glossary: neopinone = 3-methoxy-17-methyl-8,14-didehydro-4,5α-epoxymorphinan-6-one
codeinone = 3-methoxy-17-methyl-7,8-didehydro-4,5α-epoxymorphinan-6-one
Other name(s): NISO (gene name)
Systematic name: neopinone Δ8-Δ7-isomerase
Comments: The enzyme, characterized from the opium poppy (Papaver somniferum), participates in the biosynthesis of morphine. It also catalyses the isomerization of neomorphinone and morphinone.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Dastmalchi, M., Chen, X., Hagel, J.M., Chang, L., Chen, R., Ramasamy, S., Yeaman, S. and Facchini, P.J. Neopinone isomerase is involved in codeine and morphine biosynthesis in opium poppy. Nat. Chem. Biol. 15 (2019) 384–390. [DOI] [PMID: 30886433]
[EC 5.3.3.24 created 2022]
 
 
EC 5.3.4.1     
Accepted name: protein disulfide-isomerase
Reaction: Catalyses the rearrangement of -S-S- bonds in proteins
Other name(s): S-S rearrangase
Systematic name: protein disulfide-isomerase
Comments: Needs reducing agents or partly reduced enzyme; the reaction depends on sulfhydryl-disulfide interchange.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37318-49-3
References:
1.  De Lorenzo, F., Goldberger, R.F., Steers, E., Givol, D. and Anfinsen, C.B. Purification and properties of an enzyme from beef liver which catalyzes sulfhydryl-disulfide interchange in proteins. J. Biol. Chem. 241 (1966) 1562–1567. [PMID: 5946614]
2.  Fuchs, S., De Lorenzo, F. and Anfinsen, C.B. Studies on the mechanism of the enzymic catalysis of disulfide interchange in proteins. J. Biol. Chem. 242 (1967) 398–402. [PMID: 6022836]
[EC 5.3.4.1 created 1972]
 
 
EC 5.3.99.1      
Deleted entry:  hydroperoxide isomerase. Reaction due to combined action of EC 4.2.1.92 (hydroperoxide dehydratase) and EC 5.3.99.6 (allene-oxide cyclase)
[EC 5.3.99.1 created 1972, deleted 1992]
 
 
EC 5.3.99.2     
Accepted name: prostaglandin-D synthase
Reaction: (5Z,13E,15S)-9α,11α-epidioxy-15-hydroxyprosta-5,13-dienoate = (5Z,13E,15S)-9α,15-dihydroxy-11-oxoprosta-5,13-dienoate
Other name(s): prostaglandin-H2 Δ-isomerase; prostaglandin-R-prostaglandin D isomerase; PGH-PGD isomerase(5,13)-(15S)-9α,11α-epidioxy-15-hydroxyprosta-5,13-dienoate Δ-isomerase (incorrect); (5,13)-(15S)-9α,11α-epidioxy-15-hydroxyprosta-5,13-dienoate D-isomerase; prostaglandin endoperoxide Δ-isomerase; prostaglandin D synthetase
Systematic name: (5Z,13E,15S)-9α,11α-epidioxy-15-hydroxyprosta-5,13-dienoate D-isomerase
Comments: Brings about the opening of the epidioxy bridge. Some enzymes require glutathione.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 65802-85-9
References:
1.  Christ-Hazelhof, E. and Nugteren, D.H. Purification and characterisation of prostaglandin endoperoxide Δ-isomerase, a cytoplasmic, glutathione-requiring enzyme. Biochim. Biophys. Acta 572 (1979) 43–51. [DOI] [PMID: 32914]
2.  Shimizu, T., Yamamoto, S. and Hayaishi, O. Purification and properties of prostaglandin D synthetase from rat brain. J. Biol. Chem. 254 (1979) 5222–5228. [PMID: 109431]
[EC 5.3.99.2 created 1976, modified 1990]
 
 
EC 5.3.99.3     
Accepted name: prostaglandin-E synthase
Reaction: (5Z,13E)-(15S)-9α,11α-epidioxy-15-hydroxyprosta-5,13-dienoate = (5Z,13E)-(15S)-11α,15-dihydroxy-9-oxoprosta-5,13-dienoate
Other name(s): prostaglandin-H2 E-isomerase; endoperoxide isomerase; endoperoxide isomerase; prostaglandin R-prostaglandin E isomerase; prostaglandin endoperoxide E isomerase; PGE isomerase; PGH-PGE isomerase; PGE2 isomerase; prostaglandin endoperoxide E2 isomerase; prostaglandin H-E isomerase
Systematic name: (5Z,13E)-(15S)-9α,11α-epidioxy-15-hydroxyprosta-5,13-dienoate E-isomerase
Comments: Brings about the opening of the epidioxy bridge. Requires glutathione.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 52227-79-9
References:
1.  Ogino, N., Miyamoto, T., Yamamoto, S. and Hayaishi, O. Prostaglandin endoperoxide E isomerase from bovine vesicular gland microsomes, a glutathione-requiring enzyme. J. Biol. Chem. 252 (1977) 890–895. [PMID: 838703]
2.  Tanaka, Y., Ward, S.L. and Smith, W.L. Immunochemical and kinetic evidence for two different prostaglandin H-prostaglandin E isomerases in sheep vesicular gland microsomes. J. Biol. Chem. 262 (1987) 1374–1381. [PMID: 3100531]
[EC 5.3.99.3 created 1976, modified 1990]
 
 
EC 5.3.99.4     
Accepted name: prostaglandin-I synthase
Reaction: (5Z,13E,15S)-9α,11α-epidioxy-15-hydroxyprosta-5,13-dienoate = (5Z,13E,15S)-6,9α-epoxy-11α,15-dihydroxyprosta-5,13-dienoate
Other name(s): prostacyclin synthase; prostacycline synthetase; prostagladin I2 synthetase; PGI2 synthase; PGI2 synthetase; (5Z,13E)-(15S)-9α,11α-epidioxy-15-hydroxyprosta-5,13-dienoate 6-isomerase
Systematic name: (5Z,13E,15S)-9α,11α-epidioxy-15-hydroxyprosta-5,13-dienoate 6-isomerase
Comments: A cytochrome P-450 heme-thiolate enzyme. Converts prostaglandin H2 into prostaglandin I2 (prostacyclin).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 65802-86-0
References:
1.  DeWitt, D.L. and Smith, W.L. Purification of prostacyclin synthase from bovine aorta by immunoaffinity chromatography. Evidence that the enzyme is a hemoprotein. J. Biol. Chem. 258 (1983) 3285–3293. [PMID: 6338016]
2.  Ullrich, V., Castle, L. and Weber, P. Spectral evidence for the cytochrome P450 nature of prostacyclin synthetase. Biochem. Pharmacol. 30 (1981) 2033–2036. [DOI] [PMID: 7023490]
[EC 5.3.99.4 created 1984, modified 1990]
 
 
EC 5.3.99.5     
Accepted name: thromboxane-A synthase
Reaction: (5Z,13E)-(15S)-9α,11α-epidioxy-15-hydroxyprosta-5,13-dienoate = (5Z,13E)-(15S)-9α,11α-epoxy-15-hydroxythromboxa-5,13-dienoate
Other name(s): thromboxane synthase; (5Z,13E)-(15S)-9α,11α-epidioxy-15-hydroxyprosta-5,13-dienoate thromboxane-A2-isomerase
Systematic name: (5Z,13E)-(15S)-9α,11α-epidioxy-15-hydroxyprosta-5,13-dienoate isomerase
Comments: A cytochrome P-450 heme-thiolate enzyme. Converts prostaglandin H2 into thromboxane A2.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 61276-89-9
References:
1.  Shen, R.-F. and Tai, H.-H. Immunoaffinity purification and characterization of thromboxane synthase from porcine lung. J. Biol. Chem. 261 (1986) 11592–11599. [PMID: 3745158]
2.  Ullrich, V. and Haurand, M. Thromboxane synthase as a cytochrome P450 enzyme. Adv. Prostaglandin Thromboxane Res. 11 (1983) 105–110. [PMID: 6221511]
[EC 5.3.99.5 created 1984, modified 1990]
 
 
EC 5.3.99.6     
Accepted name: allene-oxide cyclase
Reaction: (9Z)-(13S)-12,13-epoxyoctadeca-9,11,15-trienoate = (15Z)-12-oxophyto-10,15-dienoate
Systematic name: (9Z)-(13S)-12,13-epoxyoctadeca-9,11,15-trienoate isomerase (cyclizing)
Comments: Allene oxides formed by the action of EC 4.2.1.92 hydroperoxide dehydratase, are converted into cyclopentenone derivatives.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 118390-59-3
References:
1.  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. [DOI] [PMID: 3178850]
[EC 5.3.99.6 created 1992]
 
 
EC 5.3.99.7     
Accepted name: styrene-oxide isomerase
Reaction: styrene oxide = phenylacetaldehyde
Other name(s): SOI
Systematic name: styrene-oxide isomerase (epoxide-cleaving)
Comments: Highly specific.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, CAS registry number: 124541-89-5
References:
1.  Hartmans, S., Smits, J.P., van der Werf, M.J., Volkering, F. and de Bont, J.A.M. Metabolism of styrene oxide and 2-phenylethanol in the styrene-degrading Xanthobacter strain 124X. Appl. Environ. Microbiol. 55 (1989) 2850–2855. [PMID: 16348047]
[EC 5.3.99.7 created 1992]
 
 
EC 5.3.99.8     
Accepted name: capsanthin/capsorubin synthase
Reaction: (1) violaxanthin = capsorubin
(2) antheraxanthin = capsanthin
For diagram of the biosynthesis of capsanthin, capsarubin and neoxanthin, click here and for diagram of carotenoid epoxide rearrangements, click here
Other name(s): CCS; ketoxanthophyll synthase; capsanthin-capsorubin synthase
Systematic name: violaxanthin—capsorubin isomerase (ketone-forming)
Comments: This multifunctional enzyme is induced during chromoplast differentiation in plants [1]. Isomerization of the epoxide ring of violaxanthin gives the cyclopentyl-ketone of capsorubin or capsanthin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 162032-85-1
References:
1.  Bouvier, F., Hugueney, P., d'Harlingue, A., Kuntz, M. and Camara, B. Xanthophyll biosynthesis in chromoplasts: isolation and molecular cloning of an enzyme catalyzing the conversion of 5,6-epoxycarotenoid into ketocarotenoid. Plant J. 6 (1994) 45–54. [DOI] [PMID: 7920703]
2.  Lefebvre, V., Kuntz, M., Camara, B. and Palloix, A. The capsanthin-capsorubin synthase gene: a candidate gene for the y locus controlling the red fruit colour in pepper. Plant Mol. Biol. 36 (1998) 785–789. [PMID: 9526511]
3.  Xu, C.J., Chen, D.M. and Zhang, S.L. [Molecular cloning of full length capsanthin/capsorubin synthase homologous gene from orange (Citrus sinensis)] Shi Yan Sheng Wu Xue Bao 34 (2001) 147–150. [PMID: 12549109] (in Chinese)
[EC 5.3.99.8 created 2005]
 
 
EC 5.3.99.9     
Accepted name: neoxanthin synthase
Reaction: violaxanthin = neoxanthin
For diagram of the biosynthesis of capsanthin, capsarubin and neoxanthin, click here and for diagram of carotenoid epoxide rearrangements, click here
Other name(s): NSY
Systematic name: violaxanthin—neoxanthin isomerase (epoxide-opening)
Comments: The opening of the epoxide ring of violaxanthin generates a chiral allene. Neoxanthin is a precursor of the plant hormone abscisic acid and the last product of carotenoid synthesis in green plants [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 318960-21-3
References:
1.  Al-Babili, S., Hugueney, P., Schledz, M., Welsch, R., Frohnmeyer, H., Laule, O. and Beyer, P. Identification of a novel gene coding for neoxanthin synthase from Solanum tuberosum. FEBS Lett. 485 (2000) 168–172. [DOI] [PMID: 11094161]
2.  Bouvier, F., d'Harlingue, A., Backhaus, R.A., Kumagai, M.H. and Camara, B. Identification of neoxanthin synthase as a carotenoid cyclase paralog. Eur. J. Biochem. 267 (2000) 6346–6352. [DOI] [PMID: 11029576]
[EC 5.3.99.9 created 2005]
 
 
EC 5.3.99.10     
Accepted name: thiazole tautomerase
Reaction: 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate = 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate
For diagram of thiamine diphosphate biosynthesis, click here
Glossary: cThz*-P = 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate
cThz-P = 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate = 4-methyl-5-[2-(phosphonooxy)ethyl]-1,3-thiazole-2-carboxylate
Other name(s): tenI (gene name)
Systematic name: 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate isomerase
Comments: The enzyme catalyses the irreversible aromatization of the thiazole moiety of 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Hazra, A.B., Han, Y., Chatterjee, A., Zhang, Y., Lai, R.Y., Ealick, S.E. and Begley, T.P. A missing enzyme in thiamin thiazole biosynthesis: identification of TenI as a thiazole tautomerase. J. Am. Chem. Soc. 133 (2011) 9311–9319. [DOI] [PMID: 21534620]
[EC 5.3.99.10 created 2012]
 
 
EC 5.3.99.11     
Accepted name: 2-keto-myo-inositol isomerase
Reaction: 2,4,6/3,5-pentahydroxycyclohexanone = 2D-2,3,5/4,6-pentahydroxycyclohexanone
For diagram of inositol catabolism, click here
Glossary: 2,4,6/3,5-pentahydroxycyclohexanone = (2R,3S,4s,5R,6S)-2,3,4,5,6-pentahydroxycyclohexanone = scyllo-inosose
Other name(s): IolI; inosose isomerase; 2KMI isomerase.
Systematic name: 2,4,6/3,5-pentahydroxycyclohexanone 2-isomerase
Comments: Requires a divalent metal ion for activity. Mn2+, Fe2+ and Co2+ can be used. The enzyme, found in the bacterium Bacillus subtilis, is part of the myo-inositol/D-chiro-inositol degradation pathway leading to acetyl-CoA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Zhang, R.G., Dementieva, I., Duke, N., Collart, F., Quaite-Randall, E., Alkire, R., Dieckman, L., Maltsev, N., Korolev, O. and Joachimiak, A. Crystal structure of Bacillus subtilis ioli shows endonuclase IV fold with altered Zn binding. Proteins 48 (2002) 423–426. [DOI] [PMID: 12112707]
2.  Yoshida, K., Yamaguchi, M., Morinaga, T., Ikeuchi, M., Kinehara, M. and Ashida, H. Genetic modification of Bacillus subtilis for production of D-chiro-inositol, an investigational drug candidate for treatment of type 2 diabetes and polycystic ovary syndrome. Appl. Environ. Microbiol. 72 (2006) 1310–1315. [DOI] [PMID: 16461681]
[EC 5.3.99.11 created 2014]
 
 
EC 5.3.99.12     
Accepted name: lachrymatory-factor synthase
Reaction: (E)-alk-1-en-1-SO-peroxol = (Z)-alkanethial oxide
Glossary: alk-1-en-1-SO-peroxol = S-alk-1-en-1-ylthiohydroperoxide
alkanethial oxide = alkylidene-λ4-sulfanone = (alkylidenesulfaniumyl)oxidanide
Other name(s): LFS
Systematic name: (E)-alk-1-en-1-SO-peroxol isomerase [(Z)-alkanethial S-oxide-forming]
Comments: The enzyme is responsible for production of the irritating lachrymatory factor that is released by onions and related species when they are chopped. It acts of the product of EC 4.4.1.4, alliin lyase. The enzyme from Allium cepa (onion) acts on (E)-prop-1-en-1-SO-peroxol and produces (Z)-propanethial oxide, while the enzyme from Allium siculum (honey garlic) acts on (E)-but-1-en-1-SO-peroxol and produces (Z)-butanethial oxide.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Norris, P.G., Nunn, A.V., Hawk, J.L. and Cox, T.M. Genetic heterogeneity in erythropoietic protoporphyria: a study of the enzymatic defect in nine affected families. J. Invest. Dermatol. 95 (1990) 260–263. [DOI] [PMID: 2384686]
2.  Imai, S., Tsuge, N., Tomotake, M., Nagatome, Y., Sawada, H., Nagata, T. and Kumagai, H. Plant biochemistry: an onion enzyme that makes the eyes water. Nature 419:685 (2002). [DOI] [PMID: 12384686]
3.  Eady, C.C., Kamoi, T., Kato, M., Porter, N.G., Davis, S., Shaw, M., Kamoi, A. and Imai, S. Silencing onion lachrymatory factor synthase causes a significant change in the sulfur secondary metabolite profile. Plant Physiol. 147 (2008) 2096–2106. [DOI] [PMID: 18583530]
4.  Kubec, R., Cody, R.B., Dane, A.J., Musah, R.A., Schraml, J., Vattekkatte, A. and Block, E. Applications of direct analysis in real time-mass spectrometry (DART-MS) in Allium chemistry. (Z)-butanethial S-oxide and 1-butenyl thiosulfinates and their S-(E)-1-butenylcysteine S-oxide precursor from Allium siculum. J. Agric. Food Chem. 58 (2010) 1121–1128. [DOI] [PMID: 20047275]
[EC 5.3.99.12 created 2021]
 
 
EC 5.4.1.1     
Accepted name: lysolecithin acylmutase
Reaction: 2-lysolecithin = 3-lysolecithin
Other name(s): lysolecithin migratase
Systematic name: lysolecithin 2,3-acylmutase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9031-24-7
References:
1.  Uziel, M. and Hanahan, D.J. An enzyme-catalyzed acyl migration: a lysolecithin migratase. J. Biol. Chem. 226 (1957) 789–798. [PMID: 13438864]
[EC 5.4.1.1 created 1961]
 
 
EC 5.4.1.2      
Transferred entry: precorrin-8X methylmutase. Now EC 5.4.99.61, precorrin-8X methylmutase
[EC 5.4.1.2 created 1999, deleted 2014]
 
 
EC 5.4.1.3     
Accepted name: 2-methylfumaryl-CoA isomerase
Reaction: 2-methylfumaryl-CoA = 3-methylfumaryl-CoA
For diagram of the 3-hydroxypropanoate cycle, click here
Glossary: 2-methylfumaryl-CoA = (E)-3-carboxy-2-methylprop-2-enoyl-CoA
3-methylfumaryl-CoA = (E)-3-carboxybut-2-enoyl-CoA
Other name(s): mesaconyl-CoA C1-C4 CoA transferase; Mct
Systematic name: 2-methylfumaryl-CoA 1,4-CoA-mutase
Comments: The enzyme, purified from the bacterium Chloroflexus aurantiacus, acts as an intramolecular CoA transferase and does not transfer CoA to free mesaconate. It is part of the 3-hydroxypropanoate cycle for carbon assimilation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
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. [DOI] [PMID: 19955419]
[EC 5.4.1.3 created 2014]
 
 
EC 5.4.1.4     
Accepted name: D-galactarolactone isomerase
Reaction: D-galactaro-1,5-lactone = D-galactaro-1,4-lactone
Other name(s): GLI
Systematic name: D-galactaro-1,5-lactone isomerase (D-galactaro-1,4-lactone-forming)
Comments: The enzyme, characterized from the bacterium Agrobacterium fabrum strain C58, belongs to the amidohydrolase superfamily. It participates in the degradation of D-galacturonate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Bouvier, J.T., Groninger-Poe, F.P., Vetting, M., Almo, S.C. and Gerlt, J.A. Galactaro δ-lactone isomerase: lactone isomerization by a member of the amidohydrolase superfamily. Biochemistry 53 (2014) 614–616. [DOI] [PMID: 24450804]
[EC 5.4.1.4 created 2015]
 
 
EC 5.4.2.1      
Transferred entry: phosphoglycerate mutase. Now recognized as two separate enzymes EC 5.4.2.11, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) and EC 5.4.2.12, phosphoglycerate mutase (2,3-diphosphoglycerate-independent)
[EC 5.4.2.1 created 1961 (EC 2.7.5.3 created 1961, incorporated 1984), deleted 2013]
 
 
EC 5.4.2.2     
Accepted name: phosphoglucomutase (α-D-glucose-1,6-bisphosphate-dependent)
Reaction: α-D-glucose 1-phosphate = D-glucose 6-phosphate
For diagram of UDP-glucose, UDP-galactose and UDP-glucuronate biosynthesis, click here
Other name(s): glucose phosphomutase (ambiguous); phosphoglucose mutase (ambiguous)
Systematic name: α-D-glucose 1,6-phosphomutase
Comments: Maximum activity is only obtained in the presence of α-D-glucose 1,6-bisphosphate. This bisphosphate is an intermediate in the reaction, being formed by transfer of a phosphate residue from the enzyme to the substrate, but the dissociation of bisphosphate from the enzyme complex is much slower than the overall isomerization. The enzyme also catalyses (more slowly) the interconversion of 1-phosphate and 6-phosphate isomers of many other α-D-hexoses, and the interconversion of α-D-ribose 1-phosphate and 5-phosphate. cf. EC 5.4.2.5, phosphoglucomutase (glucose-cofactor).
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9001-81-4
References:
1.  Joshi, J.G. and Handler, P. Phosphoglucomutase. I. Purification and properties of phosphoglucomutase from Escherichia coli. J. Biol. Chem. 239 (1964) 2741–2751. [PMID: 14216423]
2.  Najjar, V.A. Phosphoglucomutase. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), The Enzymes, 2nd edn, vol. 6, Academic Press, New York, 1962, pp. 161–178.
3.  Ray, W.J. and Roscelli, G.A. A kinetic study of the phosphoglucomutase pathway. J. Biol. Chem. 239 (1964) 1228–1236. [PMID: 14165931]
4.  Ray, W.J., Jr. and Peck, E.J., Jr. Phosphomutases. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 6, 1972, pp. 407–477.
5.  Sutherland, E.W., Cohn, M., Posternak, T. and Cori, C.F. The mechanism of the phosphoglucomutase reaction. J. Biol. Chem. 180 (1949) 1285–1295. [PMID: 18148026]
[EC 5.4.2.2 created 1961 as EC 2.7.5.1, transferred 1984 to EC 5.4.2.2]
 
 
EC 5.4.2.3     
Accepted name: phosphoacetylglucosamine mutase
Reaction: N-acetyl-α-D-glucosamine 1-phosphate = N-acetyl-D-glucosamine 6-phosphate
For diagram of UDP-N-acetylglucosamine biosynthesis, click here
Other name(s): acetylglucosamine phosphomutase; acetylglucosamine phosphomutase; acetylaminodeoxyglucose phosphomutase; phospho-N-acetylglucosamine mutase; N-acetyl-D-glucosamine 1,6-phosphomutase
Systematic name: N-acetyl-α-D-glucosamine 1,6-phosphomutase
Comments: The enzyme is activated by N-acetyl-α-D-glucosamine 1,6-bisphosphate.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9027-51-4
References:
1.  Carlson, D.M. Phosphoacetylglucosamine mutase from pig submaxillary gland. Methods Enzymol. 8 (1966) 179–182.
2.  Leloir, L.F. and Cardini, C.E. Enzymes acting on glucosamine phosphates. Biochim. Biophys. Acta 20 (1956) 33–42. [PMID: 13315346]
3.  Ray, W.J., Jr. and Peck, E.J., Jr. Phosphomutases. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 6, 1972, pp. 407–477.
4.  Reissig, J.L. and Leloir, L.F. Phosphoacetylglucosamine mutase from Neurospora. Methods Enzymol. 8 (1966) 175–178.
[EC 5.4.2.3 created 1961 as EC 2.7.5.2, transferred 1984 to EC 5.4.2.3]
 
 
EC 5.4.2.4     
Accepted name: bisphosphoglycerate mutase
Reaction: 3-phospho-D-glyceroyl phosphate = 2,3-bisphospho-D-glycerate
Other name(s): diphosphoglycerate mutase; glycerate phosphomutase; bisphosphoglycerate synthase; bisphosphoglyceromutase; biphosphoglycerate synthase; diphosphoglyceric mutase; 2,3-diphosphoglycerate mutase; phosphoglyceromutase; 2,3-diphosphoglycerate synthase; DPGM; 2,3-bisphosphoglycerate mutase; BPGM; diphosphoglyceromutase; 2,3-diphosphoglyceromutase
Systematic name: 3-phospho-D-glycerate 1,2-phosphomutase
Comments: In the direction shown, this enzyme is phosphorylated by 3-phosphoglyceroyl phosphate, to give phosphoenzyme and 3-phosphoglycerate. The latter is rephosphorylated by the enzyme to yield 2,3-bisphosphoglycerate, but this reaction is slowed by dissociation of 3-phosphoglycerate from the enzyme, which is therefore more active in the presence of added 3-phosphoglycerate. This enzyme also catalyses, slowly, the reaction of EC 5.4.2.11 [phosphoglycerate mutase (2,3-diphosphoglycerate-dependent)] and EC 5.4.2.12 [phosphoglycerate mutase (2,3-diphosphoglycerate-independent)].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37211-69-1
References:
1.  Ray, W.J., Jr. and Peck, E.J., Jr. Phosphomutases. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 6, 1972, pp. 407–477.
2.  Rose, Z.B. The purification and properties of diphosphoglycerate mutase from human erythrocytes. J. Biol. Chem. 243 (1968) 4810–4820. [PMID: 5687724]
3.  Rose, Z.B. The enzymology of 2,3-bisphosphoglycerate. Adv. Enzymol. Relat. Areas Mol. Biol. 51 (1980) 211–253. [PMID: 6255773]
[EC 5.4.2.4 created 1961 as EC 2.7.5.4, transferred 1984 to EC 5.4.2.4]
 
 
EC 5.4.2.5     
Accepted name: phosphoglucomutase (glucose-cofactor)
Reaction: α-D-glucose 1-phosphate = D-glucose 6-phosphate
Other name(s): glucose phosphomutase (ambiguous); glucose-1-phosphate phosphotransferase
Systematic name: α-D-glucose 1,6-phosphomutase (glucose-cofactor)
Comments: The enzyme is activated by D-glucose, which probably acts as an acceptor for a phosphate residue from the substrate, thus being itself converted into the product. cf. EC 5.4.2.2, phosphoglucomutase (α-D-glucose-1,6-bisphosphate-dependent).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37278-22-1
References:
1.  Fujimoto, A., Ingram, P. and Smith, R.A. D-Glucose-1-phosphate:D-glucose-6-phosphotransferase. Biochim. Biophys. Acta 96 (1965) 91–101. [DOI] [PMID: 14285271]
2.  Ray, W.J., Jr. and Peck, E.J., Jr. Phosphomutases. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 6, 1972, pp. 407–477.
[EC 5.4.2.5 created 1972 as EC 2.7.5.5, transferred 1984 to EC 5.4.2.5]
 
 
EC 5.4.2.6     
Accepted name: β-phosphoglucomutase
Reaction: β-D-glucose 1-phosphate = β-D-glucose 6-phosphate
For diagram of reaction, click here
Other name(s): β-pgm (gene name)
Systematic name: β-D-glucose 1,6-phosphomutase
Comments: The enzyme requires Mg2+ and phosphorylation of an aspartate residue at the active site. The enzyme is able to autophosphorylate itself with its substrate β-D-glucose 1-phosphate. Although this is a slow reaction, only a single turnover is required for activation. Once the phosphorylated enzyme is formed, it generates the reaction intermediate β-D-glucose 1,6-bisphosphate, which can be used to phosphorylate the enzyme in subsequent cycles [4]. cf. EC 5.4.2.2, phosphoglucomutase (α-D-glucose-1,6-bisphosphate-dependent).
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 68651-99-0
References:
1.  Ben-Zvi, R. and Schramm, M. A phosphoglucomutase specific for β-glucose 1-phosphate. J. Biol. Chem. 236 (1961) 2186–2189.
2.  Ray, W.J., Jr. and Peck, E.J., Jr. Phosphomutases. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 6, 1972, pp. 407–477.
3.  Lahiri, S.D., Zhang, G., Dunaway-Mariano, D. and Allen, K.N. The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction. Science 299 (2003) 2067–2071. [DOI] [PMID: 12637673]
4.  Dai, J., Wang, L., Allen, K.N., Radstrom, P. and Dunaway-Mariano, D. Conformational cycling in β-phosphoglucomutase catalysis: reorientation of the β-D-glucose 1,6-(Bis)phosphate intermediate. Biochemistry 45 (2006) 7818–7824. [DOI] [PMID: 16784233]
[EC 5.4.2.6 created 1984]
 
 
EC 5.4.2.7     
Accepted name: phosphopentomutase
Reaction: α-D-ribose 1-phosphate = D-ribose 5-phosphate
Other name(s): phosphodeoxyribomutase; deoxyribose phosphomutase; deoxyribomutase; phosphoribomutase; α-D-glucose-1,6-bisphosphate:deoxy-D-ribose-1-phosphate phosphotransferase; D-ribose 1,5-phosphomutase
Systematic name: α-D-ribose 1,5-phosphomutase
Comments: Also converts 2-deoxy-α-D-ribose 1-phosphate into 2-deoxy-D-ribose 5-phosphate. α-D-Ribose 1,5-bisphosphate, 2-deoxy-α-D-ribose 1,5-bisphosphate, or α-D-glucose 1,6-bisphosphate can act as cofactor.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9026-77-1
References:
1.  Hammen-Jepersen, K. and Munch-Petersen, A. Phosphodeoxyribomutase from Escherichia coli. Purification and some properties. Eur. J. Biochem. 17 (1970) 397–407. [DOI] [PMID: 4992818]
2.  Kammen, H.O. and Koo, R. Phosphopentomutases. I. Identification of two activities in rabbit tissues. J. Biol. Chem. 244 (1969) 4888–4893. [PMID: 5824563]
3.  Ray, W.J., Jr. and Peck, E.J., Jr. Phosphomutases. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 6, 1972, pp. 407–477.
[EC 5.4.2.7 created 1972 as EC 2.7.5.6, transferred 1984 to EC 5.4.2.7]
 
 
EC 5.4.2.8     
Accepted name: phosphomannomutase
Reaction: α-D-mannose 1-phosphate = D-mannose 6-phosphate
For diagram of GDP-L-fucose and GDP-mannose biosynthesis, click here
Other name(s): mannose phosphomutase; phosphomannose mutase; D-mannose 1,6-phosphomutase
Systematic name: α-D-mannose 1,6-phosphomutase
Comments: α-D-Mannose 1,6-bisphosphate or α-D-glucose 1,6-bisphosphate can act as cofactor.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 59536-73-1
References:
1.  Small, D.M. and Matheson, N.K. Phosphomannomutase and phosphoglucomutase in developing Cassia corymbosa seeds. Phytochemistry 18 (1979) 1147–1150.
[EC 5.4.2.8 created 1981 as EC 2.7.5.7, transferred 1984 to EC 5.4.2.8]
 
 
EC 5.4.2.9     
Accepted name: phosphoenolpyruvate mutase
Reaction: phosphoenolpyruvate = 3-phosphonopyruvate
For diagram of reaction, click here
Other name(s): phosphoenolpyruvate-phosphonopyruvate phosphomutase; PEP phosphomutase; phosphoenolpyruvate phosphomutase; PEPPM; PEP phosphomutase
Systematic name: phosphoenolpyruvate 2,3-phosphonomutase
Comments: Involved in the biosynthesis of the C-P bond, although the equilibrium greatly favours phosphoenolpyruvate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 115756-49-5
References:
1.  Bowman, E., McQueney, M., Barry, R.J. and Dunaway-Mariano, D. Catalysis and thermodynamics of the phosphoenolpyruvate phosphonopyruvate rearrangement - entry into the phosphonate class of naturally-occurring organo-phosphorus compounds. J. Am. Chem. Soc. 110 (1988) 5575–5576.
2.  Hikada, T., Imai, S., Hara, O., Anzai, H., Murakami, T., Nagaoka, K. and Seto, H. Carboxyphosphonoenolpyruvate phosphonomutase, a novel enzyme catalyzing C-P bond formation. J. Bacteriol. 172 (1990) 3066–3072. [DOI] [PMID: 2160937]
3.  Seidel, H.M., Freeman, S. and Knowles, J.R. Phosphonate biosynthesis: isolation of the enzyme responsible for the formation of a carbon-phosphorus bond. Nature 335 (1988) 457–458. [DOI] [PMID: 3138545]
[EC 5.4.2.9 created 1990]
 
 
EC 5.4.2.10     
Accepted name: phosphoglucosamine mutase
Reaction: α-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate
For diagram of the biosynthesis of UDP-N-acetylglucosamine, click here
Systematic name: α-D-glucosamine 1,6-phosphomutase
Comments: The enzyme is involved in the pathway for bacterial cell-wall peptidoglycan and lipopolysaccharide biosyntheses, being an essential step in the pathway for UDP-N-acetylglucosamine biosynthesis. The enzyme from Escherichia coli is activated by phosphorylation and can be autophosphorylated in vitro by α-D-glucosamine 1,6-bisphosphate, which is an intermediate in the reaction, α-D-glucose 1,6-bisphosphate or ATP. It can also catalyse the interconversion of α-D-glucose 1-phosphate and glucose 6-phosphate, although at a much lower rate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9031-92-9
References:
1.  Mengin-Lecreulx, D. and van Heijenoort, J. Characterization of the essential gene glmM encoding phosphoglucosamine mutase in Escherichia coli. J. Biol. Chem. 271 (1996) 32–39. [DOI] [PMID: 8550580]
2.  de Reuse, H., Labigne, A. and Mengin-Lecreulx, D. The Helicobacter pylori ureC gene codes for a phosphoglucosamine mutase. J. Bacteriol. 179 (1997) 3488–3493. [DOI] [PMID: 9171391]
3.  Jolly, L., Wu, S., van Heijenoort, J., de Lencastre, H., Mengin-Lecreulx, D. and Tomas, A. The femR315 gene from Staphylococcus aureus, the interruption of which results in reduced methicillin resistance, encodes a phosphoglucosamine mutase. J. Bacteriol. 179 (1997) 5321–5325. [DOI] [PMID: 9286983]
4.  Jolly, L., Ferrari, P., Blanot, D., van Heijenoort, J., Fassy, F. and Mengin-Lecreulx, D. Reaction mechanism of phosphoglucosamine mutase from Escherichia coli. Eur. J. Biochem. 262 (1999) 202–210. [DOI] [PMID: 10231382]
5.  Jolly, L., Pompeo, F., van Heijenoort, J., Fassy, F. and Mengin-Lecreulx, D. Autophosphorylation of phosphoglucosamine mutase from Escherichia coli. J. Bacteriol. 182 (2000) 1280–1285. [DOI] [PMID: 10671448]
[EC 5.4.2.10 created 2001]
 
 
EC 5.4.2.11     
Accepted name: phosphoglycerate mutase (2,3-diphosphoglycerate-dependent)
Reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate (overall reaction)
(1a) [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate = [enzyme]-Nτ-phospho-L-histidine + 2/3-phospho-D-glycerate
(1b) [enzyme]-Nτ-phospho-L-histidine + 2-phospho-D-glycerate = [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate
(1c) [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate = [enzyme]-Nτ-phospho-L-histidine + 3-phospho-D-glycerate
(1d) [enzyme]-Nτ-phospho-L-histidine + 2/3-bisphospho-D-glycerate = [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate
For diagram of the Entner-Doudoroff pathway, click here
Glossary: 2/3-phospho-D-glycerate = 2-phospho-D-glycerate or 3-phospho-D-glycerate
Other name(s): glycerate phosphomutase (diphosphoglycerate cofactor); 2,3-diphosphoglycerate dependent phosphoglycerate mutase; cofactor dependent phosphoglycerate mutase; phosphoglycerate phosphomutase (ambiguous); phosphoglyceromutase (ambiguous); monophosphoglycerate mutase (ambiguous); monophosphoglyceromutase (ambiguous); GriP mutase (ambiguous); PGA mutase (ambiguous); MPGM; PGAM; PGAM-d; PGM; dPGM
Systematic name: D-phosphoglycerate 2,3-phosphomutase (2,3-diphosphoglycerate-dependent)
Comments: The enzymes from vertebrates, platyhelminths, mollusks, annelids, crustaceans, insects, algae, some fungi and some bacteria (particularly Gram-negative) require 2,3-bisphospho-D-glycerate as a cofactor. The enzyme is activated by 2,3-bisphospho-D-glycerate by transferring a phosphate to histidine (His10 in man and Escherichia coli, His8 in Saccharomyces cerevisiae). This phosphate can be transferred to the free OH of 2-phospho-D-glycerate, followed by transfer of the phosphate already on the phosphoglycerate back to the histidine. cf. EC 5.4.2.12 phosphoglycerate mutase. The enzyme has no requirement for metal ions. This enzyme also catalyse, slowly, the reactions of EC 5.4.2.4 bisphosphoglycerate mutase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Grisolia, S. Phosphoglyceric acid mutase. Methods Enzymol. 5 (1962) 236–242.
2.  Ray, W.J., Jr. and Peck, E.J., Jr. Phosphomutases. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 6, 1972, pp. 407–477.
3.  Rose, Z.B. The enzymology of 2,3-bisphosphoglycerate. Adv. Enzymol. Relat. Areas Mol. Biol. 51 (1980) 211–253. [PMID: 6255773]
4.  Rigden, D.J., Walter, R.A., Phillips, S.E. and Fothergill-Gilmore, L.A. Sulphate ions observed in the 2.12 Å structure of a new crystal form of S. cerevisiae phosphoglycerate mutase provide insights into understanding the catalytic mechanism. J. Mol. Biol. 286 (1999) 1507–1517. [DOI] [PMID: 10064712]
5.  Bond, C.S., White, M.F. and Hunter, W.N. High resolution structure of the phosphohistidine-activated form of Escherichia coli cofactor-dependent phosphoglycerate mutase. J. Biol. Chem. 276 (2001) 3247–3253. [DOI] [PMID: 11038361]
6.  Rigden, D.J., Mello, L.V., Setlow, P. and Jedrzejas, M.J. Structure and mechanism of action of a cofactor-dependent phosphoglycerate mutase homolog from Bacillus stearothermophilus with broad specificity phosphatase activity. J. Mol. Biol. 315 (2002) 1129–1143. [DOI] [PMID: 11827481]
7.  Rigden, D.J., Littlejohn, J.E., Henderson, K. and Jedrzejas, M.J. Structures of phosphate and trivanadate complexes of Bacillus stearothermophilus phosphatase PhoE: structural and functional analysis in the cofactor-dependent phosphoglycerate mutase superfamily. J. Mol. Biol. 325 (2003) 411–420. [DOI] [PMID: 12498792]
[EC 5.4.2.11 created 1961 as EC 5.4.2.1 (EC 2.7.5.3 created 1961, incorporated 1984) transferred 2013 to EC 5.4.2.11, modified 2014]
 
 
EC 5.4.2.12     
Accepted name: phosphoglycerate mutase (2,3-diphosphoglycerate-independent)
Reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate
For diagram of the Entner-Doudoroff pathway, click here
Other name(s): cofactor independent phosphoglycerate mutase; 2,3-diphosphoglycerate-independent phosphoglycerate mutase; phosphoglycerate phosphomutase (ambiguous); phosphoglyceromutase (ambiguous); monophosphoglycerate mutase (ambiguous); monophosphoglyceromutase (ambiguous); GriP mutase (ambiguous); PGA mutase (ambiguous); iPGM; iPGAM; PGAM-i
Systematic name: D-phosphoglycerate 2,3-phosphomutase (2,3-diphosphoglycerate-independent)
Comments: The enzymes from higher plants, algae, some fungi, nematodes, sponges, coelenterates, myriapods, arachnids, echinoderms, archaea and some bacteria (particularly Gram-positive) have maximum activity in the absence of 2,3-bisphospho-D-glycerate. cf. EC 5.4.2.11 phosphoglycerate mutase (2,3-diphosphoglycerate-dependent). The enzyme contains two Mn2+ (or in some species two Co2+ ions). The reaction involves a phosphotransferase reaction to serine followed by transfer back to the glycerate at the other position. Both metal ions are involved in the reaction.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Jedrzejas, M.J., Chander, M., Setlow, P. and Krishnasamy, G. Mechanism of catalysis of the cofactor-independent phosphoglycerate mutase from Bacillus stearothermophilus. Crystal structure of the complex with 2-phosphoglycerate. J. Biol. Chem. 275 (2000) 23146–23153. [DOI] [PMID: 10764795]
2.  Rigden, D.J., Lamani, E., Mello, L.V., Littlejohn, J.E. and Jedrzejas, M.J. Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography, simulated dynamics and molecular modeling. J. Mol. Biol. 328 (2003) 909–920. [DOI] [PMID: 12729763]
3.  Zhang, Y., Foster, J.M., Kumar, S., Fougere, M. and Carlow, C.K. Cofactor-independent phosphoglycerate mutase has an essential role in Caenorhabditis elegans and is conserved in parasitic nematodes. J. Biol. Chem. 279 (2004) 37185–37190. [DOI] [PMID: 15234973]
4.  Nukui, M., Mello, L.V., Littlejohn, J.E., Setlow, B., Setlow, P., Kim, K., Leighton, T. and Jedrzejas, M.J. Structure and molecular mechanism of Bacillus anthracis cofactor-independent phosphoglycerate mutase: a crucial enzyme for spores and growing cells of Bacillus species. Biophys J 92 (2007) 977–988. [DOI] [PMID: 17085493]
5.  Nowicki, M.W., Kuaprasert, B., McNae, I.W., Morgan, H.P., Harding, M.M., Michels, P.A., Fothergill-Gilmore, L.A. and Walkinshaw, M.D. Crystal structures of Leishmania mexicana phosphoglycerate mutase suggest a one-metal mechanism and a new enzyme subclass. J. Mol. Biol. 394 (2009) 535–543. [DOI] [PMID: 19781556]
6.  Mercaldi, G.F., Pereira, H.M., Cordeiro, A.T., Michels, P.A. and Thiemann, O.H. Structural role of the active-site metal in the conformation of Trypanosoma brucei phosphoglycerate mutase. FEBS J. 279 (2012) 2012–2021. [DOI] [PMID: 22458781]
[EC 5.4.2.12 created 2013]
 
 
EC 5.4.2.13     
Accepted name: phosphogalactosamine mutase
Reaction: D-galactosamine 6-phosphate = α-D-galactosamine-1-phosphate
For diagram of UDP-N-acetylglucosamine biosynthesis, click here
Other name(s): ST0242 (locus name)
Systematic name: α-D-galactosamine 1,6-phosphomutase
Comments: The enzyme, characterized from the archaeon Sulfolobus tokodaii, is also active toward D-glucosamine 6-phosphate (cf. EC 5.4.2.10, phosphoglucosamine mutase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Dadashipour, M., Iwamoto, M., Hossain, M.M., Akutsu, J.I., Zhang, Z. and Kawarabayasi, Y. Identification of a direct biosynthetic pathway for UDP-N-acetylgalactosamine from glucosamine-6-phosphate in thermophilic crenarchaeon Sulfolobus tokodaii. J. Bacteriol. 200 (2018) . [PMID: 29507091]
[EC 5.4.2.13 created 2018]
 
 
EC 5.4.3.1      
Deleted entry:  ornithine 4,5-aminomutase. This reaction was due to a mixture of EC 5.1.1.12 (ornithine racemase) and EC 5.4.3.5 (D-ornithine 4,5-aminomutase)
[EC 5.4.3.1 created 1972, deleted 1976]
 
 
EC 5.4.3.2     
Accepted name: lysine 2,3-aminomutase
Reaction: L-lysine = (3S)-3,6-diaminohexanoate
For diagram of lysine catabolism, click here
Systematic name: L-lysine 2,3-aminomutase
Comments: This enzyme is a member of the ’AdoMet radical’ (radical SAM) family. It contains pyridoxal phosphate and a [4Fe-4S] cluster and binds an exchangeable S-adenosyl-L-methionine molecule. Activity in vitro requires a strong reductant such as dithionite and strictly anaerobic conditions. A 5′-deoxyadenosyl radical is generated during the reaction cycle by reductive cleavage of S-adenosyl-L-methionine, mediated by the iron-sulfur cluster. S-adenosyl-L-methionine is regenerated at the end of the reaction.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9075-20-1
References:
1.  Zappia, V. and Barker, H.A. Studies on lysine-2,3-aminomutase. Subunit structure and sulfhydryl groups. Biochim. Biophys. Acta 207 (1970) 505–513. [DOI] [PMID: 5452674]
2.  Aberhart, D.J., Lim, H.-J. and Weiller, B.H. Stereochemistry of lysine 2,3-aminomutase. J. Am. Chem. Soc. 103 (1981) 6750–6752.
3.  Frey, P.A. Lysine 2,3-aminomutase: is adenosylmethionine a poor man’s adenosylcobalamin. FASEB J. 7 (1993) 662–670. [PMID: 8500691]
4.  Lieder, K.W., Booker, S., Ruzicka, F.J., Beinert, H., Reed, G.H. and Frey, P.A. S-Adenosylmethionine-dependent reduction of lysine 2,3-aminomutase and observation of the catalytically functional iron-sulfur centers by electron paramagnetic resonance. Biochemistry 37 (1998) 2578–2585. [DOI] [PMID: 9485408]
5.  Lepore, B.W., Ruzicka, F.J., Frey, P.A. and Ringe, D. The x-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale. Proc. Natl. Acad. Sci. USA 102 (2005) 13819–13824. [DOI] [PMID: 16166264]
6.  Frey, P.A. and Reed, G.H. Pyridoxal-5′-phosphate as the catalyst for radical isomerization in reactions of PLP-dependent aminomutases. Biochim. Biophys. Acta 1814 (2011) 1548–1557. [DOI] [PMID: 21435400]
[EC 5.4.3.2 created 1972]
 
 
EC 5.4.3.3     
Accepted name: lysine 5,6-aminomutase
Reaction: (1) (3S)-3,6-diaminohexanoate = (3S,5S)-3,5-diaminohexanoate
(2) D-lysine = (2R,5S)-2,5-diaminohexanoate
For diagram of lysine catabolism, click here
Other name(s): β-lysine 5,6-aminomutase; β-lysine mutase; L-β-lysine 5,6-aminomutase; D-lysine 5,6-aminomutase; D-α-lysine mutase; adenosylcobalamin-dependent D-lysine 5,6-aminomutase
Systematic name: (3S)-3,6-diaminohexanoate 5,6-aminomutase
Comments: This enzyme is a member of the ‘AdoMet radical’ (radical SAM) family. It requires pyridoxal 5′-phosphate and adenosylcobalamin for activity. A 5′-deoxyadenosyl radical is generated during the reaction cycle by reductive cleavage of adenosylcobalamin, which is regenerated at the end of the reaction.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9075-69-8
References:
1.  Stadtman, T.C. and Tasi, L. A cobamide coenzyme dependent migration of the ε-amino group of D-lysine. Biochem. Biophys. Res. Commun. 28 (1967) 920–926. [DOI] [PMID: 4229021]
2.  Stadtman, T.C. and Renz, P. Anaerobic degradation of lysine. V. Some properties of the cobamide coenzyme-dependent β-lysine mutase of Clostridium sticklandii. Arch. Biochem. Biophys. 125 (1968) 226–239. [DOI] [PMID: 5649516]
3.  Morley, C.G.D. and Stadtman, T.C. Studies on the fermentation of D-α-lysine. Purification and properties of an adenosine triphosphate regulated B12-coenzyme-dependent D-α-lysine mutase complex from Clostridium sticklandii. Biochemistry 9 (1970) 4890–4900. [PMID: 5480154]
4.  Retey, J., Kunz, F., Arigoni, D. and Stadtman, T.C. Zur Kenntnis der β-Lysin-Mutase-Reaktion: mechanismus und sterischer Verlauf. Helv. Chim. Acta 61 (1978) 2989–2998.
5.  Chang, C.H. and Frey, P.A. Cloning, sequencing, heterologous expression, purification, and characterization of adenosylcobalamin-dependent D-lysine 5, 6-aminomutase from Clostridium sticklandii. J. Biol. Chem. 275 (2000) 106–114. [DOI] [PMID: 10617592]
6.  Tang, K.H., Harms, A. and Frey, P.A. Identification of a novel pyridoxal 5′-phosphate binding site in adenosylcobalamin-dependent lysine 5,6-aminomutase from Porphyromonas gingivalis. Biochemistry 41 (2002) 8767–8776. [DOI] [PMID: 12093296]
7.  Tang, K.H., Mansoorabadi, S.O., Reed, G.H. and Frey, P.A. Radical triplets and suicide inhibition in reactions of 4-thia-D- and 4-thia-L-lysine with lysine 5,6-aminomutase. Biochemistry 48 (2009) 8151–8160. [DOI] [PMID: 19634897]
8.  Berkovitch, F., Behshad, E., Tang, K.H., Enns, E.A., Frey, P.A. and Drennan, C.L. A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase. Proc. Natl. Acad. Sci. USA 101 (2004) 15870–15875. [DOI] [PMID: 15514022]
[EC 5.4.3.3 created 1972 (EC 5.4.3.4 created 1972, incorporated 2017), modified 2017]
 
 


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