The Enzyme Database

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EC 1.1.1.85     
Accepted name: 3-isopropylmalate dehydrogenase
Reaction: (2R,3S)-3-isopropylmalate + NAD+ = 4-methyl-2-oxopentanoate + CO2 + NADH + H+ (overall reaction)
(1a) (2R,3S)-3-isopropylmalate + NAD+ = (2S)-2-isopropyl-3-oxosuccinate + NADH + H+
(1b) (2S)-2-isopropyl-3-oxosuccinate = 4-methyl-2-oxopentanoate + CO2 (spontaneous)
For diagram of leucine biosynthesis, click here
Other name(s): β-isopropylmalic enzyme; β-isopropylmalate dehydrogenase; threo-Ds-3-isopropylmalate dehydrogenase; 3-carboxy-2-hydroxy-4-methylpentanoate:NAD+ oxidoreductase
Systematic name: (2R,3S)-3-isopropylmalate:NAD+ oxidoreductase
Comments: The product decarboxylates spontaneously to yield 4-methyl-2-oxopentanoate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9030-97-1
References:
1.  Burns, R.O., Umbarger, H.E. and Gross, S.R. The biosynthesis of leucine. III. The conversion of α-hydroxy-β-carboxyisocaproate to α-ketoisocaproate. Biochemistry 2 (1963) 1053. [PMID: 14087358]
2.  Parsons, S.J. and Burns, R.O. Purification and properties of β-isopropylmalate dehydrogenase. J. Biol. Chem. 244 (1969) 996–1003. [PMID: 4889950]
3.  Németh, A., Svingor, Á., Pócsik, M., Dobó, J., Magyar, C, Szilaaagyi, A., Gál, P. and Závodszky, P. Mirror image mutations reveal the significance of an intersubunit ion cluster in the stability of 3-isopropylmalate dehydrogenase. FEBS Lett. 468 (2000) 48–52. [DOI] [PMID: 10683439]
4.  Calvo, J. M., Stevens, C. M., Kalyanpur, M. G., and Umbarger, H. E. The absolute configuration of α-hydroxy-β-carboxyisocaproic acid (3-isopropylmalic acid), an intermediate in leucine biosynthesis. Biochemistry 3 (1964) 2024–2027. [PMID: 14269331]
[EC 1.1.1.85 created 1972, modified 1976]
 
 
EC 1.1.1.272     
Accepted name: D-2-hydroxyacid dehydrogenase (NADP+)
Reaction: an (R)-2-hydroxycarboxylate + NADP+ = a 2-oxocarboxylate + NADPH + H+
For diagram of coenzyme M biosynthesis, click here
Other name(s): ddh (gene name)
Systematic name: (R)-2-hydroxycarboxylate:NADP+ oxidoreductase
Comments: This enzyme, characterized from the halophilic archaeon Haloferax mediterranei and the mold Aspergillus oryzae, catalyses a stereospecific reduction of 2-oxocarboxylic acids into the corresponding D-2-hydroxycarboxylic acids. The enzyme prefers substrates with a main chain of 5 carbons (such as 4-methyl-2-oxopentanoate) to those with a shorter chain, and can use NADH with much lower efficiency. cf. EC 1.1.1.345, (D)-2-hydroxyacid dehydrogenase (NAD+).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 81210-65-3
References:
1.  Domenech, J. and Ferrer, J. A new D-2-hydroxyacid dehydrogenase with dual coenzyme-specificity from Haloferax mediterranei, sequence analysis and heterologous overexpression. Biochim. Biophys. Acta 1760 (2006) 1667–1674. [DOI] [PMID: 17049749]
2.  Shimizu, M., Yamamoto, T., Okabe, N., Sakai, K., Koide, E., Miyachi, Y., Kurimoto, M., Mochizuki, M., Yoshino-Yasuda, S., Mitsui, S., Ito, A., Murano, H., Takaya, N. and Kato, M. Novel 4-methyl-2-oxopentanoate reductase involved in synthesis of the Japanese sake flavor, ethyl leucate. Appl. Microbiol. Biotechnol. (2015) . [DOI] [PMID: 26615399]
[EC 1.1.1.272 created 2002, modified 2013]
 
 
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 1.2.1.25     
Accepted name: branched-chain α-keto acid dehydrogenase system
Reaction: 3-methyl-2-oxobutanoate + CoA + NAD+ = 2-methylpropanoyl-CoA + CO2 + NADH
Other name(s): branched-chain α-keto acid dehydrogenase complex; 2-oxoisovalerate dehydrogenase; α-ketoisovalerate dehydrogenase; 2-oxoisovalerate dehydrogenase (acylating)
Systematic name: 3-methyl-2-oxobutanoate:NAD+ 2-oxidoreductase (CoA-methylpropanoylating)
Comments: This enzyme system catalyses the oxidative decarboxylation of branched-chain α-keto acids derived from L-leucine, L-isoleucine, and L-valine to branched-chain acyl-CoAs. It belongs to the 2-oxoacid dehydrogenase system family, which also includes EC 1.2.1.104, pyruvate dehydrogenase system, EC 1.2.1.105, 2-oxoglutarate dehydrogenase system, EC 1.4.1.27, glycine cleavage system, and EC 2.3.1.190, acetoin dehydrogenase system. With the exception of the glycine cleavage system, which contains 4 components, the 2-oxoacid dehydrogenase systems share a common structure, consisting of three main components, namely a 2-oxoacid dehydrogenase (E1), a dihydrolipoamide acyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). The reaction catalysed by this system is the sum of three activities: EC 1.2.4.4, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring), EC 2.3.1.168, dihydrolipoyllysine-residue (2-methylpropanoyl)transferase, and EC 1.8.1.4, dihydrolipoyl dehydrogenase. The system also acts on (S)-3-methyl-2-oxopentanoate and 4-methyl-2-oxopentanoate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37211-61-3
References:
1.  Namba, Y., Yoshizawa, K., Ejima, A., Hayashi, T. and Kaneda, T. Coenzyme A- and nicotinamide adenine dinucleotide-dependent branched chain α-keto acid dehydrogenase. I. Purification and properties of the enzyme from Bacillus subtilis. J. Biol. Chem. 244 (1969) 4437–4447. [PMID: 4308861]
2.  Pettit, F.H., Yeaman, S.J. and Reed, L.J. Purification and characterization of branched chain α-keto acid dehydrogenase complex of bovine kidney. Proc. Natl. Acad. Sci. USA 75 (1978) 4881–4885. [DOI] [PMID: 283398]
3.  Harris, R.A., Hawes, J.W., Popov, K.M., Zhao, Y., Shimomura, Y., Sato, J., Jaskiewicz, J. and Hurley, T.D. Studies on the regulation of the mitochondrial α-ketoacid dehydrogenase complexes and their kinases. Adv. Enzyme Regul. 37 (1997) 271–293. [DOI] [PMID: 9381974]
4.  Evarsson, A., Chuang, J.L., Wynn, R.M., Turley, S., Chuang, D.T. and Hol, W.G. Crystal structure of human branched-chain α-ketoacid dehydrogenase and the molecular basis of multienzyme complex deficiency in maple syrup urine disease. Structure 8 (2000) 277–291. [PMID: 10745006]
5.  Reed, L.J. A trail of research from lipoic acid to α-keto acid dehydrogenase complexes. J. Biol. Chem. 276 (2001) 38329–38336. [DOI] [PMID: 11477096]
[EC 1.2.1.25 created 1972, modified 2019, modified 2020]
 
 
EC 1.2.4.4     
Accepted name: 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)
Reaction: 3-methyl-2-oxobutanoate + [dihydrolipoyllysine-residue (2-methylpropanoyl)transferase] lipoyllysine = [dihydrolipoyllysine-residue (2-methylpropanoyl)transferase] S-(2-methylpropanoyl)dihydrolipoyllysine + CO2
For diagram of oxo-acid-dehydrogenase complexes, click here
Glossary: dihydrolipoyl group
thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): 2-oxoisocaproate dehydrogenase; 2-oxoisovalerate (lipoate) dehydrogenase; 3-methyl-2-oxobutanoate dehydrogenase (lipoamide); 3-methyl-2-oxobutanoate:lipoamide oxidoreductase (decarboxylating and acceptor-2-methylpropanoylating); α-keto-α-methylvalerate dehydrogenase; α-ketoisocaproate dehydrogenase; α-ketoisocaproic dehydrogenase; α-ketoisocaproic-α-keto-α-methylvaleric dehydrogenase; α-ketoisovalerate dehydrogenase; α-oxoisocaproate dehydrogenase; BCKDH (ambiguous); BCOAD; branched chain keto acid dehydrogenase; branched-chain (-2-oxoacid) dehydrogenase (BCD); branched-chain 2-keto acid dehydrogenase; branched-chain 2-oxo acid dehydrogenase; branched-chain α-keto acid dehydrogenase; branched-chain α-oxo acid dehydrogenase; branched-chain keto acid dehydrogenase; branched-chain ketoacid dehydrogenase; dehydrogenase, 2-oxoisovalerate (lipoate); dehydrogenase, branched chain α-keto acid
Systematic name: 3-methyl-2-oxobutanoate:[dihydrolipoyllysine-residue (2-methylpropanoyl)transferase]-lipoyllysine 2-oxidoreductase (decarboxylating, acceptor-2-methylpropanoylating)
Comments: Contains thiamine diphosphate. It acts not only on 3-methyl-2-oxobutanaoate, but also on 4-methyl-2-oxopentanoate and (S)-3-methyl-2-oxopentanoate, so that it acts on the 2-oxo acids that derive from the action of transaminases on valine, leucine and isoleucine. It is a component of the multienzyme 3-methyl-2-oxobutanoate dehydrogenase complex in which multiple copies of it are bound to a core of molecules of EC 2.3.1.168, dihydrolipoyllysine-residue (2-methylpropanoyl)transferase, which also binds multiple copies of EC 1.8.1.4, dihydrolipoyl dehydrogenase. It does not act on free lipoamide or lipoyllysine, but only on the lipoyllysine residue in EC 2.3.1.168.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9082-72-8
References:
1.  Bowden, J.A. and Connelly, J.L. Branched chain α-keto acid metabolism. II. Evidence for the common identity of α-ketoisocaproic acid and α-keto-β-methyl-valeric acid dehydrogenases. J. Biol. Chem. 243 (1968) 3526–3531. [PMID: 5656388]
2.  Connelly, J.L., Danner, D.J. and Bowden, J.A. Branched chain α-keto acid metabolism. I. Isolation, purification, and partial characterization of bovine liver α-ketoisocaproic:α-keto-β-methylvaleric acid dehydrogenase. J. Biol. Chem. 243 (1968) 1198–1203. [PMID: 5689906]
3.  Danner, D.J., Lemmon, S.K., Beharse, J.C. and Elsas, L.J., II Purification and characterization of branched chain α-ketoacid dehydrogenase from bovine liver mitochondria. J. Biol. Chem. 254 (1979) 5522–5526. [PMID: 447664]
4.  Pettit, F.H., Yeaman, S.J. and Reed, L.J. Purification and characterization of branched chain α-keto acid dehydrogenase complex of bovine kidney. Proc. Natl. Acad. Sci. USA 75 (1978) 4881–4885. [DOI] [PMID: 283398]
5.  Perham, R.N. Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu. Rev. Biochem. 69 (2000) 961–1004. [DOI] [PMID: 10966480]
[EC 1.2.4.4 created 1972 (EC 1.2.4.3 created 1972, incorporated 1978), modified 2003]
 
 
EC 1.4.1.9     
Accepted name: leucine dehydrogenase
Reaction: L-leucine + H2O + NAD+ = 4-methyl-2-oxopentanoate + NH3 + NADH + H+
Other name(s): L-leucine dehydrogenase; L-leucine:NAD+ oxidoreductase, deaminating; LeuDH
Systematic name: L-leucine:NAD+ oxidoreductase (deaminating)
Comments: Also acts on isoleucine, valine, norvaline and norleucine.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9082-71-7
References:
1.  Sanwal, B.D. and Zink, M.W. L-Leucine dehydrogenase of Bacillus cereus. Arch. Biochem. Biophys. 94 (1961) 430–435. [DOI] [PMID: 13746411]
2.  Zink, M.W. and Sanwal, B.D. The distribution and substrate specificity of L-leucine dehydrogenase. Arch. Biochem. Biophys. 99 (1962) 72–77.
[EC 1.4.1.9 created 1972]
 
 
EC 2.3.1.182      
Transferred entry: (R)-citramalate synthase. Now classified as EC 2.3.3.21, (R)-citramalate synthase.
[EC 2.3.1.182 created 2007, deleted 2021]
 
 
EC 2.3.3.21     
Accepted name: (R)-citramalate synthase
Reaction: acetyl-CoA + pyruvate + H2O = CoA + (2R)-2-hydroxy-2-methylbutanedioate
Glossary: (2R)-2-hydroxy-2-methylbutanedioate = (2R)-2-methylmalate = (–)-citramalate
3-methyl-2-oxobutanoate = α-ketoisovalerate
2-oxobutanoate = α-ketobutyrate
4-methyl-2-oxopentanoate = α-ketoisocaproate
2-oxohexanoate = α-ketopimelate
2-oxoglutarate = α-ketoglutarate
Other name(s): CimA
Comments: One of the enzymes involved in a pyruvate-derived pathway for isoleucine biosynthesis that is found in some bacterial and archaeal species [1,2]. The enzyme can be inhibited by isoleucine, the end-product of the pathway, but not by leucine [2]. The enzyme is highly specific for pyruvate as substrate, as the 2-oxo acids 3-methyl-2-oxobutanoate, 2-oxobutanoate, 4-methyl-2-oxopentanoate, 2-oxohexanoate and 2-oxoglutarate cannot act as substrate [1,2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Howell, D.M., Xu, H. and White, R.H. (R)-citramalate synthase in methanogenic archaea. J. Bacteriol. 181 (1999) 331–333. [DOI] [PMID: 9864346]
2.  Xu, H., Zhang, Y., Guo, X., Ren, S., Staempfli, A.A., Chiao, J., Jiang, W. and Zhao, G. Isoleucine biosynthesis in Leptospira interrogans serotype 1ai strain 56601 proceeds via a threonine-independent pathway. J. Bacteriol. 186 (2004) 5400–5409. [DOI] [PMID: 15292141]
[EC 2.3.3.21 created 2007 as EC 2.3.1.182, transferred 2021 to EC 2.3.3.21]
 
 
EC 2.6.1.6     
Accepted name: leucine transaminase
Reaction: L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate
For diagram of reaction, click here, for diagram of leucine biosynthesis, click here and for diagram of mechanism, click here
Other name(s): L-leucine aminotransferase; leucine 2-oxoglutarate transaminase; leucine aminotransferase; leucine-α-ketoglutarate transaminase
Systematic name: L-leucine:2-oxoglutarate aminotransferase
Comments: A pyridoxal-phosphate protein. This enzyme differs from EC 2.6.1.42, branched-chain-amino-acid transaminase, in that it does not act on L-valine or L-isoleucine, although it does act on L-methionine. The mitochondrial form from rat liver differs in physical characteristics from the cytoplasmic form.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9030-37-9
References:
1.  Aki, K., Ogawa, K. and Ichihara, A. Transaminases of branched chain amino acids. IV. Purification and properties of two enzymes from rat liver. Biochim. Biophys. Acta 159 (1968) 276–284. [DOI] [PMID: 4968655]
2.  Ikeda, T., Konishi, Y. and Ichihara, A. Transaminase of branched chain amino acids. XI. Leucine (methionine) transaminase of rat liver mitochondria. Biochim. Biophys. Acta 445 (1976) 622–631. [DOI] [PMID: 974100]
[EC 2.6.1.6 created 1961, modified 1982]
 
 
EC 2.6.1.42     
Accepted name: branched-chain-amino-acid transaminase
Reaction: L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate
For diagram of reaction, click here, of leucine biosynthesis click here, of isoleucine and valine biosynthesis, click here, of coenzyme-A biosynthesis, click here and for diagram of mechanism, click here
Other name(s): transaminase B; branched-chain amino acid aminotransferase; branched-chain amino acid-glutamate transaminase; branched-chain aminotransferase; L-branched chain amino acid aminotransferase; glutamate-branched-chain amino acid transaminase
Systematic name: branched-chain-amino-acid:2-oxoglutarate aminotransferase
Comments: Also acts on L-isoleucine and L-valine, and thereby differs from EC 2.6.1.6, leucine transaminase, which does not. It also differs from EC 2.6.1.66, valine—pyruvate transaminase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9054-65-3
References:
1.  Aki, K., Ogawa, K. and Ichihara, A. Transaminases of branched chain amino acids. IV. Purification and properties of two enzymes from rat liver. Biochim. Biophys. Acta 159 (1968) 276–284. [DOI] [PMID: 4968655]
2.  Aki, K., Yokojima, A. and Ichihara, A. Transaminase of branched chain amino acids. VI. Purification and properties of the hog brain enzyme. J. Biochem. (Tokyo) 65 (1969) 539–544. [PMID: 4979711]
3.  Ichihara, A. and Koyama, E. Transaminase of branched chain amino acids. I. Branched chain amino acids-α-ketoglutarate transaminase. J. Biochem. (Tokyo) 59 (1966) 160–169. [PMID: 5943594]
4.  Taylor, R.T. and Jenkins, W.T. Leucine aminotransferase. II. Purification and characterization. J. Biol. Chem. 241 (1966) 4396–4405. [PMID: 5922965]
5.  Rudman, D. and Meister, A. Transamination in Escherichia coli. J. Biol. Chem. 200 (1953) 591–604. [PMID: 13034817]
[EC 2.6.1.42 created 1972]
 
 


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