EC 5.1.1 Acting on Amino Acids and Derivatives
EC 5.1.2 Acting on Hydroxy Acids and Derivatives
EC 5.1.3 Acting on Carbohydrates and Derivatives
EC 5.1.99 Acting on Other Compounds
Accepted name: alanine racemase
Reaction: L-alanine = D-alanine
Other name(s): L-alanine racemase
Systematic name: alanine racemase
Comments: A pyridoxal-phosphate protein.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9024-06-0
References:
1. Marr, A.G. and Wilson, P.W. The alanine racemase of Brucella abortus. Arch. Biochem. Biophys. 49 (1954) 424-433.
2. Wood, W.A. Amino acid racemases. Methods Enzymol. 2 (1955) 212-217.
3. Wood, W.A. and Gunsalus, I.C. D-Alanine formation: a racemase in Streptococcus faecalis. J. Biol. Chem. 190 (1951) 403-416.
Accepted name: methionine racemase
Reaction: L-methionine = D-methionine
Systematic name: methionine racemase
Comments: A pyridoxal-phosphate protein.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9024-07-1
References:
1. Kallio, R.E. and Larson, A.D. Methionine degradation by a species of Pseudomonas, in McElroy, W.D. and Glass, H.B. (Eds.), A Symposium on Amino Acid Metabolism, Johns Hopkins Press, Baltimore, 1955, pp. 616-634.
Accepted name: glutamate racemase
Reaction: L-glutamate = D-glutamate
Systematic name: glutamate racemase
Comments: A pyridoxal-phosphate protein.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9024-08-2
References:
1. Glaser, L. Glutamic acid racemase from Lactobacillus arabinosus. J. Biol. Chem. 235 (1960) 2095-2098.
Accepted name: proline racemase
Reaction: L-proline = D-proline
Systematic name: proline racemase
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9024-09-3
References:
1. Stadtman, T.C. and Elliott, P. Studies on the enzymic reduction of amino acids. II. Purification and properties of a D-proline reductase and a proline racemase from Clostridium sticklandii. J. Biol. Chem. 228 (1957) 983-997.
Accepted name: lysine racemase
Reaction: L-lysine = D-lysine
Systematic name: lysine racemase
Comments: The enzyme is involved in a lysine catabolic pathway.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9024-10-6
References:
1. Huang, H.T. and Davisson, J.W. Distribution of lysine racemase in bacteria. J. Bacteriol. 76 (1958) 495-498. [PMID: 13598707]
2. Huang, H.T. dl-Lysine production by lysine racemase. Patent US2944943, Chem. Abstr., 54 (1960), 20073.
3. Chen, I.C., Lin, W.D., Hsu, S.K., Thiruvengadam, V. and Hsu, W.H. Isolation and characterization of a novel lysine racemase from a soil metagenomic library. Appl. Environ. Microbiol. 75 (2009) 5161-5166. [PMID: 19502445]
4. Kato, S., Hemmi, H. and Yoshimura, T. Lysine racemase from a lactic acid bacterium, Oenococcus oeni: structural basis of substrate specificity. J. Biochem. 152 (2012) 505-508. [PMID: 23035128]
Accepted name: threonine racemase
Reaction: L-threonine = D-threonine
Glossary: D-threonine = (2R,3S)-2-amino-3-hydroxybutanoic acid
Systematic name: threonine racemase
Comments: Inverts both chiral centres.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9024-11-7
References:
1. Amos, H. A racemase for threonine in Escherichia coli. J. Am. Chem. Soc. 76 (1954) 3858 only.
Accepted name: diaminopimelate epimerase
Reaction: LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate
For diagram click here.
Systematic name: LL-2,6-diaminoheptanedioate 2-epimerase
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9024-22-0
References:
1. Antia, M., Hoare, D.S. and Work, W. The stereoisomers of αε-diaminopimelic acid. 3. Properties and distribution of diaminopimelic acid racemase, an enzyme causing interconversion of the LL and meso isomers. Biochem. J. 65 (1957) 448-459.
Accepted name: 4-hydroxyproline epimerase
Reaction: trans-4-hydroxy-L-proline = cis-4-hydroxy-D-proline
For reaction pathway click here.
Other name(s): hydroxyproline epimerase; hydroxyproline 2-epimerase; L-hydroxyproline epimerase
Systematic name: 4-hydroxyproline 2-epimerase
Comments: Also interconverts trans-4-hydroxy-D-proline and cis-4-hydroxy-L-proline.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9024-23-1
References:
1. Adams, E. and Norton, I.L. Purification and properties of inducible hydroxyproline 2-epimerase from Pseudomonas. J. Biol. Chem. 239 (1964) 1525-1535.
Accepted name: arginine racemase
Reaction: L-arginine = D-arginine
Systematic name: arginine racemase
Comments: A pyridoxal-phosphate protein.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37290-94-1
References:
1. Yorifuji, T., Ogata, K. and Soda, K. Crystalline arginine racemase. Biochem. Biophys. Res. Commun. 34 (1969) 760-764. [PMID: 5779761]
Accepted name: amino-acid racemase
Reaction: An L-amino acid = a D-amino acid
Other name(s): L-amino acid racemase
Systematic name: amino-acid racemase
Comments: A pyridoxal-phosphate protein.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9068-61-5
References:
1. Soda, K. and Osumi, T. Crystalline amino acid racemase with low substrate specificity. Biochem. Biophys. Res. Commun. 35 (1969) 363-368. [PMID: 5788493]
Accepted name: phenylalanine racemase (ATP-hydrolysing)
Reaction: ATP + L-phenylalanine + H2O = AMP + diphosphate + D-phenylalanine
Other name(s): phenylalanine racemase; phenylalanine racemase (adenosine triphosphate-hydrolysing); gramicidin S synthetase I
Systematic name: phenylalanine racemase (ATP-hydrolysing)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37290-95-2
References:
1. Yamada, M. and Kurahashi, K. Further purification and properties of adenosine triphosphate-dependent phenylalanine racemase of Bacillus brevis Nagano. J. Biochem. (Tokyo) 66 (1969) 529-540. [PMID: 5354026]
Accepted name: ornithine racemase
Reaction: L-ornithine = D-ornithine
Systematic name: ornithine racemase
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 62213-28-9
References:
1. Chen, H.P., Lin, C.F., Lee, Y.J., Tsay, S.S. and Wu, S.H. Purification and properties of ornithine racemase from Clostridium sticklandii. J. Bacteriol. 182 (2000) 2052-2054. [PMID: 10715017]
Accepted name: aspartate racemase
Reaction: L-aspartate = D-aspartate
Other name(s): D-aspartate racemase; McyF
Systematic name: aspartate racemase
Comments: Also acts, at half the rate, on L-alanine.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37237-56-2
References:
1. Lamont, H.C., Staudenbauer, W.L. and Strominger, J.L. Partial purification and characterization of an aspartate racemase from Streptococcus faecalis. J. Biol. Chem. 247 (1972) 5103-5106. [PMID: 4626916]
2. Yamauchi, T., Choi, S.Y., Okada, H., Yohda, M., Kumagai, H., Esaki, N. and Soda, K. Properties of aspartate racemase, a pyridoxal 5'-phosphate-independent amino acid racemase. J. Biol. Chem. 267 (1992) 18361-18364. [PMID: 1526977]
3. Liu, L., Iwata, K., Kita, A., Kawarabayasi, Y., Yohda, M. and Miki, K. Crystal structure of aspartate racemase from Pyrococcus horikoshii OT3 and its implications for molecular mechanism of PLP-independent racemization. J. Mol. Biol. 319 (2002) 479-489. [PMID: 12051922]
4. Sielaff, H., Dittmann, E., Tandeau De Marsac, N., Bouchier, C., von Dühren, H., Börner, T. and Schwecke, T. The mcyF gene of the microcystin biosynthetic gene cluster from Microcystis aeruginosa encodes an aspartate racemase. Biochem. J. 373 (2003) 909-916. [PMID: 12713441]
5. Yamashita, T., Ashiuchi, M., Ohnishi, K., Kato, S., Nagata, S. and Misono, H. Molecular identification of monomeric aspartate racemase from Bifidobacterium bifidum. Eur. J. Biochem. 271 (2004) 4798-4803. [PMID: 15606767]
Accepted name: nocardicin A epimerase
Reaction: (1) isonocardicin C = nocardicin C
(2) isonocardicin A = nocardicin A
For diagram of reaction click here.
Other name(s): isonocardicin A epimerase; nocJ (gene name)
Systematic name: nocardicin-C epimerase
Comments: Requires pyridoxal 5'-phosphate. The enzyme, characterized from the bacterium Nocardia uniformis, is involved in the biosynthesis of the monolactam antibiotic nocardicin A. It catalyses the epimerization of the amino group at position 9' from (S)- configuration to (R)-. The enzyme can act on both isonocardicin A and isonocardicin C, but the in vivo substrate appears to be the latter [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 118246-75-6
References:
1. Wilson, B.A., Bantia, S., Salituro, G.M., Reeve, A.M. and Townsend, C.A. Cell-free biosynthesis of nocardicin A from nocardicin E and S-adenosylmethionine. J. Am. Chem. Soc. 110 (1988) 8238-8239.
2. Kelly, W.L. and Townsend, C.A. Mutational analysis and characterization of nocardicin C-9' epimerase. J. Biol. Chem. 279 (2004) 38220-38227. [PMID: 15252031]
3. Kelly, W.L. and Townsend, C.A. Mutational analysis of nocK and nocL in the nocardicin a producer Nocardia uniformis. J. Bacteriol. 187 (2005) 739-746. [PMID: 15629944]
Accepted name: 2-aminohexano-6-lactam racemase
Reaction: (S)-2-aminohexano-6-lactam = (R)-2-aminohexano-6-lactam
Glossary: (S)-2-aminohexano-6-lactam = L-lysine 1,6-lactam
Other name(s): α-amino-ε-caprolactam racemase
Systematic name: 2-aminohexano-6-lactam racemase
Comments: Contains pyridoxal 5'-phosphate. Also racemises 2-aminopentano-5-lactam (α-amino-δ-valerolactam) and 2-amino-4-thiahexano-6-lactam (where S replaces CH2 of C-4). It does not catalyse the racemisation of α-amino acids but has some transaminase activity with them.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 52652-64-9
References:
1. Ahmed, S.A., Esaki, N., Tanaka, H., Soda, K. L-α-Amino-β-thio-ε-caprolactam, a new sulfur-containing substrate for α-amino-ε-caprolactam racemase. FEBS Lett. 174 (1984) 76-79.
2. Ahmed, S.A., Esaki, N., Tanaka, H., Soda, K. Mechanism of α-amino-ε-caprolactam racemase reaction. Biochemistry 25 (1986) 385-388. [PMID: 3955003]
3. Okazaki, S., Suzuki, A., Mizushima, T., Kawano, T., Komeda, H., Asano, Y. and Yamane, T. The novel structure of a pyridoxal 5'-phosphate-dependent fold-type I racemase, α-amino-ε-caprolactam racemase from Achromobacter obae. Biochemistry 48 (2009) 941–950. [PMID: 19146406]
Accepted name: protein-serine epimerase
Reaction: [protein]-L-serine = [protein]-D-serine
Other name(s): protein-serine racemase
Systematic name: [protein]-serine epimerase
Comments: the enzyme specifically interconverts the configuration of Ser-46 of the peptide ω-agatoxin-KT, found in the venom of the funnel web spider, Agelenopsis aperta, but not that of the other serine residue, Ser-28.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 169592-52-3
References:
1. Shikata, Y., Watanabe, T., Teramoto, T., Inoue, A., Kawakami, Y., Nishizawa, Y., Katayama, K., Kuwada, M. Isolation and characterization of a peptide isomerase from funnel web spider venom. J. Biol. Chem. 270 (1995) 16719-16723. [PMID: 7622482]
Accepted name: isopenicillin-N epimerase
Reaction: isopenicillin N = penicillin N
For diagram click here.
Systematic name: penicillin-N 5-amino-5-carboxypentanoyl-epimerase
Comments: This enzyme contains pyridoxal phosphate. Epimerization at C-5 of the 5-amino-5-carboxypentanoyl group to form penicillin N is required to make a substrate for EC 1.14.20.1, deactoxycephalosporin-C synthase, to produce cephalosporins. Forms part of the penicillin biosynthesis pathway (for pathway, click here).
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 88201-43-8
References:
1. Usui, S. and Yu, C.-A. Purification and properties of isopenicillin-N epimerase from Streptomyces clavuligerus. Biochim. Biophys. Acta 999 (1989) 78-85. [PMID: 2804141]
2. Laiz, L., Liras, P., Castro, J.M. and Martín, J.F. Purification and characterization of the isopenicillin-N epimerase from Nocardia lactamdurans. J. Gen. Microbiol. 136 (1990) 663-671.
3. Cantwell, C., Beckmann, R., Whiteman, P., Queener, S.W. and Abraham, E.P. Isolation of deacetoxycephalosporin-c from fermentation broths of Penicillium chrysogenum transformants - construction of a new fungal biosynthetic-pathway. Proc. R. Soc. Lond. B Biol. Sci. 248 (1992) 283-289. [PMID: 1354366]
4. Yeh, W.K., Ghag, S.K. and Queener, S.W. Enzymes for epimerization of isopenicillin N, ring expansion of penicillin N, and 3'-hydroxylation of deacetoxycephalosporin C. Function, evolution, refolding, and enzyme engineering. Ann. N.Y. Acad. Sci. 672 (1992) 396-408.
Accepted name: serine racemase
Reaction: L-serine = D-serine
Other name(s): SRR
Systematic name: serine racemase
Comments: A pyridoxal-phosphate protein that is highly selective for L-serine as substrate. D-Serine is found in type-II astrocytes in mammalian brain, where it appears to be an endogenous ligand of the glycine site of N-methyl-D-aspartate (NMDA) receptors [1,2]. The reaction can also occur in the reverse direction but does so more showly at physiological serine concentrations [4].
Links to other databases: BRENDA, EXPASY, KEGG, PDB, Metacyc, PDB, CAS registry number:
References:
1. Wolosker, H., Blackshaw, S. and Snyder, S.H. Serine racemase: a glial enzyme synthesizing D-serine to regulate glutamate-N-methyl-D-aspartate neurotransmission. Proc. Natl. Acad. Sci. USA 96 (1999) 13409-13414. [PMID: 10557334]
2. Wolosker, H., Sheth, K.N., Takahashi, M., Mothet, J.P., Brady, R.O., Jr., Ferris, C.D. and Snyder, S.H. Purification of serine racemase: biosynthesis of the neuromodulator D-serine. Proc. Natl. Acad. Sci. USA 96 (1999) 721-725. [PMID: 9892700]
3. De Miranda, J., Santoro, A., Engelender, S. and Wolosker, H. Human serine racemase: moleular cloning, genomic organization and functional analysis. Gene 256 (2000) 183-188. [PMID: 11054547]
4. Foltyn, V.N., Bendikov, I., De Miranda, J., Panizzutti, R., Dumin, E., Shleper, M., Li, P., Toney, M.D., Kartvelishvily, E. and Wolosker, H. Serine racemase modulates intracellular D-serine levels through an α,β-elimination activity. J. Biol. Chem. 280 (2005) 1754-1763. [PMID: 15536068]
Accepted name: O-ureido-serine racemase
Reaction: O-ureido-L-serine = O-ureido-D-serine
Glossary: O-ureido-L-serine = (2S)-2-amino-3-[(carbamoylamino)oxy]propanoate
O-ureido-D-serine = (2R)-2-amino-3-[(carbamoylamino)oxy]propanoate
Other name(s): dcsC (gene name)
Systematic name: (2S)-2-amino-3-[(carbamoylamino)oxy]propanoate 2-epimerase
Comments: The enzyme employs a two-base mechanism, with a thiolate-thiol pair in the active site. It participates in the biosynthetic pathway of D-cycloserine, an antibiotic substance produced by several Streptomyces species.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Kumagai, T., Koyama, Y., Oda, K., Noda, M., Matoba, Y. and Sugiyama, M. Molecular cloning and heterologous expression of a biosynthetic gene cluster for the antitubercular agent D-cycloserine produced by Streptomyces lavendulae. Antimicrob. Agents Chemother. 54 (2010) 1132-1139. [PMID: 20086163]
2. Dietrich, D., van Belkum, M.J. and Vederas, J.C. Characterization of DcsC, a PLP-independent racemase involved in the biosynthesis of D-cycloserine. Org. Biomol. Chem. 10 (2012) 2248-2254. [PMID: 22307920]
Accepted name: L-Ala-D/L-Glu epimerase
Reaction: L-alanyl-D-glutamate = L-alanyl-L-glutamate
Other name(s): YkfB; YcjG; AEE; AE epimerase
Systematic name: L-alanyl-D-glutamate epimerase
Comments: The enzyme, characterized from the bacteria Escherichia coli and Bacillus subtilis, is involved in the recycling of the murein peptide, of which L-Ala-D-Glu is a component. In vitro the enzyme from Escherichia coli epimerizes several L-Ala-L-X dipeptides with broader specificity than the enzyme from Bacillus subtilis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Schmidt, D.M., Hubbard, B.K. and Gerlt, J.A. Evolution of enzymatic activities in the enolase superfamily: functional assignment of unknown proteins in Bacillus subtilis and Escherichia coli as L-Ala-D/L-Glu epimerases. Biochemistry 40 (2001) 15707-15715. [PMID: 11747447]
2. Gulick, A.M., Schmidt, D.M., Gerlt, J.A. and Rayment, I. Evolution of enzymatic activities in the enolase superfamily: crystal structures of the L-Ala-D/L-Glu epimerases from Escherichia coli and Bacillus subtilis. Biochemistry 40 (2001) 15716-15724. [PMID: 11747448]
Accepted name: isoleucine 2-epimerase
Reaction: L-isoleucine = D-allo-isoleucine
Other name(s): BCAA racemase
Systematic name: isoleucine 2-epimerase
Comments: A pyridoxal phosphate protein. The enzyme, characterized from the bacterium Lactobacillus buchneri, specifically catalyses racemization of nonpolar amino acids at the C-2 position.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Mutaguchi, Y., Ohmori, T., Wakamatsu, T., Doi, K. and Ohshima, T. Identification, purification, and characterization of a novel amino acid racemase, isoleucine 2-epimerase, from Lactobacillus species. J. Bacteriol. 195 (2013) 5207-5215. [PMID: 24039265]
Accepted name: 4-hydroxyproline betaine 2-epimerase
Reaction: (1) trans-4-hydroxy-L-proline betaine = cis-4-hydroxy-D-proline betaine
(2) L-proline betaine = D-proline betaine
Glossary: trans-4-hydroxy-L-proline betaine = (2S,4R)-4-hydroxy-1,1-dimethylpyrrolidinium-2-carboxylate
cis-4-hydroxy-D-proline betaine = (2R,4R)-4-hydroxy-1,1-dimethylpyrrolidinium-2-carboxylate
L-proline betaine = (2S)-1,1-dimethylpyrrolidinium-2-carboxylate
D-proline betaine = (2R)-1,1-dimethylpyrrolidinium-2-carboxylate
Other name(s): hpbD (gene name); Hyp-B 2-epimerase; (4R)-4-hydroxyproline betaine 2-epimerase
Systematic name: 4-hydroxyproline betaine 2-epimerase
Comments: The enzyme, characterized from the bacteria Pelagibaca bermudensis and Paracoccus denitrificans, specifically catalyses racemization of trans-4-hydroxy-L-proline betaine and L-proline betaine at the C-2 position.
Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Zhao, S., Kumar, R., Sakai, A., Vetting, M.W., Wood, B.M., Brown, S., Bonanno, J.B., Hillerich, B.S., Seidel, R.D., Babbitt, P.C., Almo, S.C., Sweedler, J.V., Gerlt, J.A., Cronan, J.E. and Jacobson, M.P. Discovery of new enzymes and metabolic pathways by using structure and genome context. Nature 502 (2013) 698-702. [PMID: 24056934]
2. Kumar, R., Zhao, S., Vetting, M.W., Wood, B.M., Sakai, A., Cho, K., Solbiati, J., Almo, S.C., Sweedler, J.V., Jacobson, M.P., Gerlt, J.A. and Cronan, J.E. Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine. MBio 5 (2014) e00933. [PMID: 24520058]
Accepted name: UDP-N-acetyl-α-D-muramoyl-L-alanyl-L-glutamate epimerase
Reaction: ATP + UDP-N-acetyl-α-D-muramoyl-L-alanyl-L-glutamate + H2O = AMP + diphosphate + UDP-N-acetyl-α-D-muramoyl-L-alanyl-D-glutamate
Other name(s): murL (gene name); UDP-MurNAc-L-Ala-L-Glu epimerase
Systematic name: UDP-N-acetyl-α-D-muramoyl-L-alanyl-L-glutamate L-glutamate-epimerase
Comments: The enzyme, characterized from the bacterium Xanthomonas oryzae, catalyses epimerization of the terminal L-glutamate in UDP-N-acetyl-α-D-muramoyl-L-alanyl-L-glutamate. The reaction proceeds only in one direction and involves an adenylated intermediate. The combined activity of this enzyme and EC 6.3.2.53, UDP-N-acetylmuramoyl-L-alanine—L-glutamate ligase, provides an alternative route for incorporating D-glutamate into peptidoglycan, replacing the more common combination of EC 5.1.1.3, glutamate racemase, and EC 6.3.2.9, UDP-N-acetylmuramoyl-L-alanine—D-glutamate ligase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Feng, R., Satoh, Y., Ogasawara, Y., Yoshimura, T. and Dairi, T. A glycopeptidyl-glutamate epimerase for bacterial peptidoglycan biosynthesis. J. Am. Chem. Soc. 139 (2017) 4243-4245. [PMID: 28294606]
Accepted name: histidine racemase
Reaction: L-histidine = D-histidine
For diagram of reaction click here.
Glossary: staphylopine = (2S)-4-{[(1R)-1-carboxy-2-(1H-imidazol-4-yl)ethyl]amino}-2-[(1-carboxyethyl)amino]butanoate
Other name(s): cntK (gene name)
Systematic name: histidine racemase
Comments: The enzyme, characterized from the bacterium Staphylococcus aureus, participates in the biosynthesis of the metallophore staphylopine, which is involved in the acquisition of nickel, copper, and cobalt.
Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Ghssein, G., Brutesco, C., Ouerdane, L., Fojcik, C., Izaute, A., Wang, S., Hajjar, C., Lobinski, R., Lemaire, D., Richaud, P., Voulhoux, R., Espaillat, A., Cava, F., Pignol, D., Borezee-Durant, E. and Arnoux, P. Biosynthesis of a broad-spectrum nicotianamine-like metallophore in Staphylococcus aureus. Science 352 (2016) 1105-1109. [PMID: 27230378]
Accepted name: N-acetyl-D-glutamate racemase
Reaction: N-acetyl-D-glutamate = N-acetyl-L-glutamate
Other name(s): dgcA (gene name)
Systematic name: N-acetyl-glutamate racemase
Comments: The enzyme, present in bacteria and archaea, participates in a pathway for the degradation of D-glutamate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Yu, Y., Wang, P., Cao, H.Y., Teng, Z.J., Zhu, Y., Wang, M., McMinn, A., Chen, Y., Xiang, H., Zhang, Y.Z., Chen, X.L. and Zhang, Y.Q. Novel D-glutamate catabolic pathway in marine Proteobacteria and halophilic archaea. ISME J. (2023) . [PMID: 36690779]
EC 5.1.2.7 tagaturonate epimerase
Accepted name: lactate racemase
Reaction: (S)-lactate = (R)-lactate
Other name(s): lacticoracemase; hydroxyacid racemase; lactic acid racemase
Systematic name: lactate racemase
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9024-05-9
References:
1. Huennekens, F.M., Mahler, H.R. and Nordmann, J. Studies on the cyclophorase system. XVII. The occurrence and properties of an α-hydroxy acid racemase. Arch. Biochem. 30 (1951) 77-89.
2. Kitahara, K., Obayashi, A. and Fukui, S. Racemase I cell-free racemase. Enzymologia 15 (1953) 259-266.
3. Goffin, P., Deghorain, M., Mainardi, J.L., Tytgat, I., Champomier-Verges, M.C., Kleerebezem, M. and Hols, P. Lactate racemization as a rescue pathway for supplying D-lactate to the cell wall biosynthesis machinery in Lactobacillus plantarum. J. Bacteriol. 187 (2005) 6750-6761. [PMID: 16166538]
4. Desguin, B., Goffin, P., Viaene, E., Kleerebezem, M., Martin-Diaconescu, V., Maroney, M.J., Declercq, J.P., Soumillion, P. and Hols, P. Lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system. Nat Commun 5 (2014) 3615. [PMID: 24710389]
5. Desguin, B., Zhang, T., Soumillion, P., Hols, P., Hu, J. and Hausinger, R.P. A tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase. Science 349 (2015) 66-69. [PMID: 26138974]
6. Yu, M.J. and Chen, S.L. From NAD+ to nickel pincer complex: a significant cofactor evolution presented by lactate racemase. Chemistry 23 (2017) 7545-7557. [PMID: 28374531]
Accepted name: mandelate racemase
Reaction: (S)-mandelate = (R)-mandelate
Glossary: mandelate = 2-hydroxy-2-phenylacetate
Systematic name: mandelate racemase
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9024-04-8
References:
1. Gunsalus, C.F., Stanier, R.Y. and Gunsalus, I.C. The enzymatic conversion of mandelic acid to benzoic acid. III. Fractionation and properties of the soluble enzymes. J. Bacteriol. 66 (1953) 548-553.
Accepted name: 3-hydroxybutyryl-CoA epimerase
Reaction: (S)-3-hydroxybutanoyl-CoA = (R)-3-hydroxybutanoyl-CoA
Other name(s): 3-hydroxybutyryl coenzyme A epimerase; 3-hydroxyacyl-CoA epimerase
Systematic name: 3-hydroxybutanoyl-CoA 3-epimerase
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9024-21-9
References:
1. Stern, J.R., del Campillo, A. and Lehninger, A.L. Enzymatic racemization of β-hydroxybutyryl-S-CoA and the stereospecificity of enzymes of the fatty acid cycle. J. Am. Chem. Soc. 77 (1955) 1073-1074.
2. Wakil, S.J. D(–)β-Hydroxybutyryl CoA dehydrogenase. Biochim. Biophys. Acta 18 (1955) 314-315.
Accepted name: acetoin racemase
Reaction: (S)-acetoin = (R)-acetoin
Other name(s): acetylmethylcarbinol racemase
Systematic name: acetoin racemase
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37318-32-4
References:
1. Taylor, M.B. and Juni, E. Stereoisomeric specificities of 2,3-butanediol dehydrogenases. Biochim. Biophys. Acta 39 (1960) 448-457.
Accepted name: tartrate epimerase
Reaction: (R,R)-tartrate = meso-tartrate
Other name(s): tartaric racemase
Systematic name: tartrate epimerase
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37318-33-5
References:
1. Ranjan, S., Patnaik, K.K. and Laloraya, M.M. Enzymic conversion of meso-tartrate to dextro-tartrate in tamarind. Naturwissenschaften 48 (1961) 406 only.
Accepted name: isocitrate epimerase
Reaction: (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate = (1S,2S)-1-hydroxypropane-1,2,3-tricarboxylate
For diagram 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.
Accepted name: tagaturonate epimerase
Reaction: D-tagaturonate = D-fructuronate
Other name(s): fructuronate epimerase; tagaturonate/fructuronate epimerase; UxaE
Systematic name: D-tagaturonate 3-epimerase
Comments: The enzyme, present in bacteria, is involved in a degradation pathway of D-galacturonate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Rodionova, I.A., Scott, D.A., Grishin, N.V., Osterman, A.L. and Rodionov, D.A. Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima. Environ Microbiol 14 (2012) 2920-2934. [PMID: 22925190]