The Enzyme Database

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EC 1.1.1.345     
Accepted name: D-2-hydroxyacid dehydrogenase (NAD+)
Reaction: an (R)-2-hydroxycarboxylate + NAD+ = a 2-oxocarboxylate + NADH + H+
Other name(s): LdhA; HdhD; D-2-hydroxyisocaproate dehydrogenase; R-HicDH; D-HicDH; (R)-2-hydroxy-4-methylpentanoate:NAD+ oxidoreductase; (R)-2-hydroxyisocaproate dehydrogenase; D-mandelate dehydrogenase (ambiguous)
Systematic name: (R)-2-hydroxycarboxylate:NAD+ oxidoreductase
Comments: The enzymes, characterized from bacteria (Peptoclostridium difficile, Enterococcus faecalis and from lactic acid bacteria) prefer substrates with a main chain of 5 carbons (such as 4-methyl-2-oxopentanoate) to those with a shorter chain. It also utilizes phenylpyruvate. The enzyme from the halophilic archaeon Haloferax mediterranei prefers substrates with a main chain of 3-4 carbons (pyruvate and 2-oxobutanoate). cf. EC 1.1.1.272, (D)-2-hydroxyacid dehydrogenase (NADP+).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Dengler, U., Niefind, K., Kiess, M. and Schomburg, D. Crystal structure of a ternary complex of D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 Å resolution. J. Mol. Biol. 267 (1997) 640–660. [DOI] [PMID: 9126843]
2.  Bonete, M.J., Ferrer, J., Pire, C., Penades, M. and Ruiz, J.L. 2-Hydroxyacid dehydrogenase from Haloferax mediterranei, a D-isomer-specific member of the 2-hydroxyacid dehydrogenase family. Biochimie 82 (2000) 1143–1150. [DOI] [PMID: 11120357]
3.  Kim, J., Darley, D., Selmer, T. and Buckel, W. Characterization of (R)-2-hydroxyisocaproate dehydrogenase and a family III coenzyme A transferase involved in reduction of L-leucine to isocaproate by Clostridium difficile. Appl. Environ. Microbiol. 72 (2006) 6062–6069. [DOI] [PMID: 16957230]
4.  Wada, Y., Iwai, S., Tamura, Y., Ando, T., Shinoda, T., Arai, K. and Taguchi, H. A new family of D-2-hydroxyacid dehydrogenases that comprises D-mandelate dehydrogenases and 2-ketopantoate reductases. Biosci. Biotechnol. Biochem. 72 (2008) 1087–1094. [DOI] [PMID: 18391442]
5.  Chambellon, E., Rijnen, L., Lorquet, F., Gitton, C., van Hylckama Vlieg, J.E., Wouters, J.A. and Yvon, M. The D-2-hydroxyacid dehydrogenase incorrectly annotated PanE is the sole reduction system for branched-chain 2-keto acids in Lactococcus lactis. J. Bacteriol. 191 (2009) 873–881. [DOI] [PMID: 19047348]
6.  Miyanaga, A., Fujisawa, S., Furukawa, N., Arai, K., Nakajima, M. and Taguchi, H. The crystal structure of D-mandelate dehydrogenase reveals its distinct substrate and coenzyme recognition mechanisms from those of 2-ketopantoate reductase. Biochem. Biophys. Res. Commun. 439 (2013) 109–114. [DOI] [PMID: 23954635]
[EC 1.1.1.345 created 2013]
 
 
EC 1.1.1.379     
Accepted name: (R)-mandelate dehydrogenase
Reaction: (R)-mandelate + NAD+ = phenylglyoxylate + NADH + H+
Glossary: (R)-mandelate = D-mandelate
Other name(s): ManDH2; D-ManDH2; D-mandelate dehydrogenase (ambiguous)
Systematic name: (R)-mandelate:NAD+ 2-oxidoreductase
Comments: The enzyme, found in bacteria and fungi, can also accept a number of substituted mandelate derivatives, such as 3-hydroxymandelate, 4-hydroxymandelate, 2-methoxymandelate, 4-hydroxy-3-methoxymandelate and 3-hydroxy-4-methoxymandelate. The enzyme has no activity with (S)-mandelate (cf. EC 1.1.99.31, (S)-mandelate dehydrogenase) [1,2]. The enzyme transfers the pro-R-hydrogen from NADH [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Baker, D.P. and Fewson, C.A. Purification and characterization of D(–)-mandelate dehydrogenase from Rhodotorula graminis. Microbiology 135 (1989) 2035–2044.
2.  Baker, D.P., Kleanthous, C., Keen, J.N., Weinhold, E. and Fewson, C.A. Mechanistic and active-site studies on D(–)-mandelate dehydrogenase from Rhodotorula graminis. Biochem. J. 281 (1992) 211–218. [PMID: 1731758]
[EC 1.1.1.379 created 2014]
 
 
EC 1.1.3.19     
Accepted name: 4-hydroxymandelate oxidase (decarboxylating)
Reaction: (S)-4-hydroxymandelate + O2 = 4-hydroxybenzaldehyde + CO2 + H2O2
Glossary: (S)-4-hydroxymandelate = (S)-2-hydroxy-2-(4-hydroxyphenyl)acetate
Other name(s): L-4-hydroxymandelate oxidase (decarboxylating); (S)-2-hydroxy-2-(4-hydroxyphenyl)acetate:oxygen 1-oxidoreductase; (S)-4-hydroxymandelate:oxygen 1-oxidoreductase; 4-hydroxymandelate oxidase
Systematic name: (S)-4-hydroxymandelate:oxygen 1-oxidoreductase (decarboxylating)
Comments: A flavoprotein (FAD), requires Mn2+. The enzyme from the bacterium Pseudomonas putida is involved in the degradation of mandelate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 60976-30-9
References:
1.  Bhat, S.G. and Vaidyanathan, C.S. Purification and properties of L-4-hydroxymandelate oxidase from Pseudomonas convexa. Eur. J. Biochem. 68 (1976) 323–331. [DOI] [PMID: 976259]
[EC 1.1.3.19 created 1984, modified 2014]
 
 
EC 1.1.3.46     
Accepted name: 4-hydroxymandelate oxidase
Reaction: (S)-4-hydroxymandelate + O2 = 2-(4-hydroxyphenyl)-2-oxoacetate + H2O2
Glossary: (S)-4-hydroxymandelate = (S)-2-hydroxy-2-(4-hydroxyphenyl)acetate
2-(4-hydroxyphenyl)-2-oxoacetate = 4-hydroxyphenylglyoxylate = (4-hydroxyphenyl)(oxo)acetate
L-(4-hydroxyphenyl)glycine = (S)-4-hydroxyphenylglycine
L-(3,5-dihydroxyphenyl)glycine = (S)-3,5-dihydroxyphenylglycine
Other name(s): 4HmO; HmO
Systematic name: (S)-4-hydroxymandelate:oxygen 1-oxidoreductase
Comments: A flavoprotein (FMN). The enzyme from the bacterium Amycolatopsis orientalis is involved in the biosynthesis of L-(4-hydroxyphenyl)glycine and L-(3,5-dihydroxyphenyl)glycine, two non-proteinogenic amino acids occurring in the vancomycin group of antibiotics.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hubbard, B.K., Thomas, M.G. and Walsh, C.T. Biosynthesis of L-p-hydroxyphenylglycine, a non-proteinogenic amino acid constituent of peptide antibiotics. Chem. Biol. 7 (2000) 931–942. [DOI] [PMID: 11137816]
2.  Li, T.L., Choroba, O.W., Charles, E.H., Sandercock, A.M., Williams, D.H. and Spencer, J.B. Characterisation of a hydroxymandelate oxidase involved in the biosynthesis of two unusual amino acids occurring in the vancomycin group of antibiotics. Chem. Commun. (Camb.) (2001) 1752–1753. [PMID: 12240298]
[EC 1.1.3.46 created 2014]
 
 
EC 1.1.99.31     
Accepted name: (S)-mandelate dehydrogenase
Reaction: (S)-mandelate + acceptor = phenylglyoxylate + reduced acceptor
For diagram of reaction, click here
Glossary: (S)-mandelate = (S)-2-hydroxy-2-phenylacetate
phenylglyoxylate = benzoylformate = 2-oxo-2-phenylacetate
Other name(s): MDH (ambiguous)
Systematic name: (S)-mandelate:acceptor 2-oxidoreductase
Comments: This enzyme is a member of the FMN-dependent α-hydroxy-acid oxidase/dehydrogenase family [1]. While all enzymes of this family oxidize the (S)-enantiomer of an α-hydroxy acid to an α-oxo acid, the ultimate oxidant (oxygen, intramolecular heme or some other acceptor) depends on the particular enzyme. This enzyme transfers the electron pair from FMNH2 to a component of the electron transport chain, most probably ubiquinone [1,2]. It is part of a metabolic pathway in Pseudomonads that allows these organisms to utilize mandelic acid, derivatized from the common soil metabolite amygdalin, as the sole source of carbon and energy [2]. The enzyme has a large active-site pocket and preferentially binds substrates with longer sidechains, e.g. 2-hydroxyoctanoate rather than 2-hydroxybutyrate [1]. It also prefers substrates that, like (S)-mandelate, have β unsaturation, e.g. (indol-3-yl)glycolate compared with (indol-3-yl)lactate [1]. Esters of mandelate, such as methyl (S)-mandelate, are also substrates [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, UM-BBD, CAS registry number: 9067-95-2
References:
1.  Lehoux, I.E. and Mitra, B. (S)-Mandelate dehydrogenase from Pseudomonas putida: mechanistic studies with alternate substrates and pH and kinetic isotope effects. Biochemistry 38 (1999) 5836–5848. [DOI] [PMID: 10231535]
2.  Dewanti, A.R., Xu, Y. and Mitra, B. Role of glycine 81 in (S)-mandelate dehydrogenase from Pseudomonas putida in substrate specificity and oxidase activity. Biochemistry 43 (2004) 10692–10700. [DOI] [PMID: 15311930]
3.  Dewanti, A.R., Xu, Y. and Mitra, B. Esters of mandelic acid as substrates for (S)-mandelate dehydrogenase from Pseudomonas putida: implications for the reaction mechanism. Biochemistry 43 (2004) 1883–1890. [DOI] [PMID: 14967029]
[EC 1.1.99.31 created 2006]
 
 
EC 1.13.11.46     
Accepted name: 4-hydroxymandelate synthase
Reaction: 4-hydroxyphenylpyruvate + O2 = (S)-4-hydroxymandelate + CO2
For diagram of 4-hydroxyphenylpyruvate metabolites, click here
Glossary: (S)-4-hydroxymandelate = (S)-2-hydroxy-2-(4-hydroxyphenyl)acetate
Other name(s): 4-hydroxyphenylpyruvate dioxygenase II
Systematic name: (S)-4-hydroxyphenylpyruvate:oxygen oxidoreductase (decarboxylating)
Comments: Requires Fe2+. Involved in the biosynthesis of the vancomycin group of glycopeptide antibiotics.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 280566-04-3
References:
1.  Hubbard, B.K., Thomas, M.G. and Walsh, C.T. Biosynthesis of L-p-hydroxyphenylglycine, a non-proteinogenic amino acid constituent of peptide antibiotics. Chem. Biol. 7 (2000) 931–942. [DOI] [PMID: 11137816]
2.  Choroba, O.W., Williams, D.H. and Spencer, J.B. Biosynthesis of the vancomycin group of antibiotics: involvement of an unusual dioxygenase in the pathway to (S)-4-hydroxyphenylglycine. J. Am. Chem. Soc. 122 (2000) 5389–5390.
[EC 1.13.11.46 created 2001]
 
 
EC 1.13.11.83     
Accepted name: 4-hydroxy-3-prenylphenylpyruvate oxygenase
Reaction: 3-dimethylallyl-4-hydroxyphenylpyruvate + O2 = 3-dimethylallyl-4-hydroxymandelate + CO2
For diagram of 3-dimethylallyl-4-hydroxybenzoate biosynthesis, click here
Other name(s): CloR
Systematic name: 3-dimethylallyl-4-hydroxyphenylpyruvate:oxygen 1,2-oxidoreductase (3-dimethylallyl-4-hydroxymandelate forming)
Comments: Requires non-heme-Fe(II). Isolated from the bacterium Streptomyces roseochromogenes DS 12976. A bifunctional enzyme involved in clorobiocin biosynthesis that also catalyses the activity of EC 1.13.12.23, 3-dimethylallyl-4-hydroxybenzoate synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Pojer, F., Kahlich, R., Kammerer, B., Li, S.M. and Heide, L. CloR, a bifunctional non-heme iron oxygenase involved in clorobiocin biosynthesis. J. Biol. Chem. 278 (2003) 30661–30668. [DOI] [PMID: 12777382]
[EC 1.13.11.83 created 2017]
 
 
EC 1.13.12.23     
Accepted name: 4-hydroxy-3-prenylbenzoate synthase
Reaction: 3-dimethylallyl-4-hydroxymandelate + O2 = 3-dimethylallyl-4-hydroxybenzoate + CO2 + H2O
For diagram of 3-dimethylallyl-4-hydroxybenzoate biosynthesis, click here
Other name(s): CloR; novR (gene name)
Systematic name: 3-dimethylallyl-4-hydroxymandelate:oxygen oxidoreductase (3-dimethylallyl-4-hydroxybenzoate forming)
Comments: Isolated from the bacterium Streptomyces roseochromogenes DS 12976. A bifunctional enzyme involved in clorobiocin biosynthesis that also catalyses the activity of EC 1.13.11.83, 3-dimethylallyl-4-hydroxyphenylpyruvate oxygenase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Pojer, F., Kahlich, R., Kammerer, B., Li, S.M. and Heide, L. CloR, a bifunctional non-heme iron oxygenase involved in clorobiocin biosynthesis. J. Biol. Chem. 278 (2003) 30661–30668. [DOI] [PMID: 12777382]
[EC 1.13.12.23 created 2017]
 
 
EC 1.14.16.6     
Accepted name: mandelate 4-monooxygenase
Reaction: (S)-2-hydroxy-2-phenylacetate + a 5,6,7,8-tetrahydropteridine + O2 = (S)-4-hydroxymandelate + a 4a-hydroxy-5,6,7,8-tetrahydropteridine
Glossary: (S)-4-hydroxymandelate = (S)-2-hydroxy-2-(4-hydroxyphenyl)acetate
Other name(s): L-mandelate 4-hydroxylase; mandelic acid 4-hydroxylase
Systematic name: (S)-2-hydroxy-2-phenylacetate,tetrahydropteridine:oxygen oxidoreductase (4-hydroxylating)
Comments: Requires Fe2+. The enzyme has been characterized from the bacterium Pseudomonas putida. The 4a-hydroxytetrahydropteridine formed can dehydrate to 6,7-dihydropteridine, both spontaneously and by the action of EC 4.2.1.96, 4a-hydroxytetrahydrobiopterin dehydratase. The 6,7-dihydropteridine must be enzymically reduced back to tetrahydropteridine, by EC 1.5.1.34, 6,7-dihydropteridine reductase, before it slowly rearranges into the more stable but inactive compound 7,8-dihydropteridine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 39459-82-0
References:
1.  Bhat, S.G. and Vaidyanathan, C.S. Purifications and properties of L-mandelate-4-hydroxylase from Pseudomonas convexa. Arch. Biochem. Biophys. 176 (1976) 314–323. [DOI] [PMID: 9909]
[EC 1.14.16.6 created 1984, modified 2020]
 
 
EC 3.5.1.86     
Accepted name: mandelamide amidase
Reaction: (R)-mandelamide + H2O = (R)-mandelate + NH3
Glossary: (R)-mandelate = (R)-2-hydroxy-2-phenylacetate
Other name(s): Pseudomonas mandelamide hydrolase
Systematic name: mandelamide hydrolase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Yamamoto, K., Oishi, K., Fujimatsu, I. and Komatsu, K. Production of R-(-)-mandelic acid from mandelonitrile by Alcaligenes faecalis ATCC 8750. Appl. Environ. Microbiol. 57 (1991) 3028–3032. [PMID: 1660699]
[EC 3.5.1.86 created 2000]
 
 
EC 5.1.2.2     
Accepted name: mandelate racemase
Reaction: (S)-mandelate = (R)-mandelate
Glossary: mandelate = 2-hydroxy-2-phenylacetate
Systematic name: mandelate racemase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, UM-BBD, 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. [PMID: 13108854]
[EC 5.1.2.2 created 1961]
 
 


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