The Enzyme Database

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EC 1.1.1.434     
Accepted name: 2-dehydro-3-deoxy-L-fuconate 4-dehydrogenase
Reaction: 2-dehydro-3-deoxy-L-fuconate + NAD+ = 2,4-didehydro-3-deoxy-L-fuconate + NADH + H+
For diagram of L-fucose catabolism, click here
Glossary: 2-dehydro-3-deoxy-L-fuconate = (4S,5S)-4,5-dihydroxy-2-oxohexanoate
2,4-didehydro-3-deoxy-L-fuconate = (5S)-5-hydroxy-2,4-dioxohexanoate
Systematic name: 2-dehydro-3-deoxy-L-fuconate:NAD+ 4-oxidoreductase
Comments: The enzyme, originally described from the bacterium Xanthomonas campestris pv. campestris, participates in an L-fucose degradation pathway. It can also act on 2-dehydro-3-deoxy-L-galactonate and 2-dehydro-3-deoxy-D-pentonate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Yew, W.S., Fedorov, A.A., Fedorov, E.V., Rakus, J.F., Pierce, R.W., Almo, S.C. and Gerlt, J.A. Evolution of enzymatic activities in the enolase superfamily: L-fuconate dehydratase from Xanthomonas campestris. Biochemistry 45 (2006) 14582–14597. [DOI] [PMID: 17144652]
2.  Watanabe, S., Fukumori, F., Nishiwaki, H., Sakurai, Y., Tajima, K. and Watanabe, Y. Novel non-phosphorylative pathway of pentose metabolism from bacteria. Sci. Rep. 9:155 (2019). [DOI] [PMID: 30655589]
[EC 1.1.1.434 created 2022]
 
 
EC 1.2.1.87     
Accepted name: propanal dehydrogenase (CoA-propanoylating)
Reaction: propanal + CoA + NAD+ = propanoyl-CoA + NADH + H+
Other name(s): BphJ
Systematic name: propanal:NAD+ oxidoreductase (CoA-propanoylating)
Comments: The enzyme forms a bifunctional complex with EC 4.1.3.43, 4-hydroxy-2-oxohexanoate aldolase, with a tight channel connecting the two subunits [1,2,3]. Also acts, more slowly, on glycolaldehyde and butanal. In Pseudomonas species the enzyme forms a bifunctional complex with EC 4.1.3.39, 4-hydroxy-2-oxovalerate aldolase. The enzymes from the bacteria Burkholderia xenovorans and Thermus thermophilus also perform the reaction of EC 1.2.1.10, acetaldehyde dehydrogenase (acetylating). NADP+ can replace NAD+ with a much slower rate [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Baker, P., Pan, D., Carere, J., Rossi, A., Wang, W. and Seah, S.Y.K. Characterization of an aldolase-dehydrogenase complex that exhibits substrate channeling in the polychlorinated biphenyls degradation pathway. Biochemistry 48 (2009) 6551–6558. [DOI] [PMID: 19476337]
2.  Carere, J., Baker, P. and Seah, S.Y.K. Investigating the molecular determinants for substrate channeling in BphI-BphJ, an aldolase-dehydrogenase complex from the polychlorinated biphenyls degradation pathway. Biochemistry 50 (2011) 8407–8416. [DOI] [PMID: 21838275]
3.  Baker, P., Hillis, C., Carere, J. and Seah, S.Y.K. Protein-protein interactions and substrate channeling in orthologous and chimeric aldolase-dehydrogenase complexes. Biochemistry 51 (2012) 1942–1952. [DOI] [PMID: 22316175]
[EC 1.2.1.87 created 2013]
 
 
EC 1.4.3.14     
Accepted name: L-lysine oxidase
Reaction: L-lysine + O2 + H2O = 6-amino-2-oxohexanoate + NH3 + H2O2
Other name(s): L-lysine α-oxidase; L-lysyl-α-oxidase
Systematic name: L-lysine:oxygen 2-oxidoreductase (deaminating)
Comments: Also acts, more slowly, on L-ornithine, L-phenylalanine, L-arginine and L-histidine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 70132-14-8
References:
1.  Kusakabe, H., Kodama, K., Kuninaka, A., Yoshino, H., Misono, H. and Soda, K. A new antitumor enzyme, L-lysine α-oxidase from Trichoderma viride. Purification and enzymological properties. J. Biol. Chem. 255 (1980) 976–981. [PMID: 6101334]
2.  Lukasheva, E.V. and Berezov, T.T. L-Lysine α-oxidase: physicochemical and biological properties. Biochemistry (Mosc.) 67 (2002) 1152–1158. [PMID: 12460113]
[EC 1.4.3.14 created 1981]
 
 
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 2.6.1.67     
Accepted name: 2-aminohexanoate transaminase
Reaction: L-2-aminohexanoate + 2-oxoglutarate = 2-oxohexanoate + L-glutamate
For diagram of reaction, click here and for mechanism, click here
Other name(s): norleucine transaminase; norleucine (leucine) aminotransferase; leucine L-norleucine: 2-oxoglutarate aminotransferase
Systematic name: L-2-aminohexanoate:2-oxoglutarate aminotransferase
Comments: A pyridoxal-phosphate protein. Also acts on L-leucine and, more slowly, on L-isoleucine, L-2-aminopentanoate and L-aspartate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 111310-35-1
References:
1.  Der Garabedian, P.A. and Vermeersch, J.J. Candida L-norleucine, leucine:2-oxoglutarate aminotransferase. Purification and properties. Eur. J. Biochem. 167 (1987) 141–147. [DOI] [PMID: 3622507]
[EC 2.6.1.67 created 1989]
 
 
EC 4.1.1.43     
Accepted name: phenylpyruvate decarboxylase
Reaction: phenylpyruvate = phenylacetaldehyde + CO2
Glossary: phenylpyruvate = 3-phenyl-2-oxopropanoate
Other name(s): phenylpyruvate carboxy-lyase; phenylpyruvate carboxy-lyase (phenylacetaldehyde-forming)
Systematic name: 3-phenyl-2-oxopropanoate carboxy-lyase (phenylacetaldehyde-forming)
Comments: The enzyme from the bacterium Azospirillum brasilense also acts on some other substrates, including (indol-3-yl)pyruvate, with much lower efficiency. However, it only possesses classical Michaelis-Menten kinetics with phenylpyruvate. Aliphatic 2-oxo acids longer that 2-oxohexanoate are not substrates. cf. EC 4.1.1.74, indolepyruvate decarboxylase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37289-45-5
References:
1.  Asakawa, T., Wada, H. and Yamano, T. Enzymatic conversion of phenylpyruvate to phenylacetate. Biochim. Biophys. Acta 170 (1968) 375–391. [DOI] [PMID: 4303395]
2.  Spaepen, S., Versees, W., Gocke, D., Pohl, M., Steyaert, J. and Vanderleyden, J. Characterization of phenylpyruvate decarboxylase, involved in auxin production of Azospirillum brasilense. J. Bacteriol. 189 (2007) 7626–7633. [PMID: 17766418]
[EC 4.1.1.43 created 1972]
 
 
EC 4.1.2.52     
Accepted name: 4-hydroxy-2-oxoheptanedioate aldolase
Reaction: 4-hydroxy-2-oxoheptanedioate = pyruvate + succinate semialdehyde
Other name(s): 2,4-dihydroxyhept-2-enedioate aldolase; HHED aldolase; 4-hydroxy-2-ketoheptanedioate aldolase; HKHD aldolase; HpcH; HpaI; 4-hydroxy-2-oxoheptanedioate succinate semialdehyde lyase (pyruvate-forming)
Systematic name: 4-hydroxy-2-oxoheptanedioate succinate-semialdehyde-lyase (pyruvate-forming)
Comments: Requires Co2+ or Mn2+ for activity. The enzyme is also able to catalyse the aldol cleavage of 4-hydroxy-2-oxopentanoate and 4-hydroxy-2-oxohexanoate, and can use 2-oxobutanoate as carbonyl donor, with lower efficiency. In the reverse direction, is able to condense a range of aldehyde acceptors with pyruvate. The enzyme from the bacterium Escherichia coli produces a racemic mixture of (4R)- and (4S)-hydroxy-2-oxoheptanedioate [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Wang, W. and Seah, S.Y. Purification and biochemical characterization of a pyruvate-specific class II aldolase, HpaI. Biochemistry 44 (2005) 9447–9455. [DOI] [PMID: 15996099]
2.  Rea, D., Fulop, V., Bugg, T.D. and Roper, D.I. Structure and mechanism of HpcH: a metal ion dependent class II aldolase from the homoprotocatechuate degradation pathway of Escherichia coli. J. Mol. Biol. 373 (2007) 866–876. [DOI] [PMID: 17881002]
3.  Wang, W. and Seah, S.Y. The role of a conserved histidine residue in a pyruvate-specific class II aldolase. FEBS Lett. 582 (2008) 3385–3388. [DOI] [PMID: 18775708]
4.  Wang, W., Baker, P. and Seah, S.Y.K. Comparison of two metal-dependent pyruvate aldolases related by convergent evolution: substrate specificity, kinetic mechanism, and substrate channeling. Biochemistry 49 (2010) 3774–3782. [DOI] [PMID: 20364820]
[EC 4.1.2.52 created 2013]
 
 
EC 4.1.3.39     
Accepted name: 4-hydroxy-2-oxovalerate aldolase
Reaction: (S)-4-hydroxy-2-oxopentanoate = acetaldehyde + pyruvate
For diagram of 3-phenylpropanoate catabolism, click here, for diagram of catechol catabolism (meta ring cleavage), click here and for diagram of cinnamate catabolism, click here
Glossary: (S)-4-hydroxy-2-oxopentanoate = (S)-4-hydroxy-2-oxovalerate
Other name(s): 4-hydroxy-2-ketovalerate aldolase; HOA; DmpG; 4-hydroxy-2-oxovalerate pyruvate-lyase; 4-hydroxy-2-oxopentanoate pyruvate-lyase; BphI; 4-hydroxy-2-oxopentanoate pyruvate-lyase (acetaldehyde-forming)
Systematic name: (S)-4-hydroxy-2-oxopentanoate pyruvate-lyase (acetaldehyde-forming)
Comments: Requires Mn2+ for maximal activity [1]. The enzyme from the bacterium Pseudomonas putida is also stimulated by NADH [1]. In some bacterial species the enzyme forms a bifunctional complex with EC 1.2.1.10, acetaldehyde dehydrogenase (acetylating). The enzymes from the bacteria Burkholderia xenovorans and Thermus thermophilus also perform the reaction of EC 4.1.3.43, 4-hydroxy-2-oxohexanoate aldolase [4,5].
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37325-52-3
References:
1.  Manjasetty, B.A., Powlowski, J. and Vrielink, A. Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate. Proc. Natl. Acad. Sci. USA 100 (2003) 6992–6997. [DOI] [PMID: 12764229]
2.  Powlowski, J., Sahlman, L. and Shingler, V. Purification and properties of the physically associated meta-cleavage pathway enzymes 4-hydroxy-2-ketovalerate aldolase and aldehyde dehydrogenase (acylating) from Pseudomonas sp. strain CF600. J. Bacteriol. 175 (1993) 377–385. [DOI] [PMID: 8419288]
3.  Manjasetty, B.A., Croteau, N., Powlowski, J. and Vrielink, A. Crystallization and preliminary X-ray analysis of dmpFG-encoded 4-hydroxy-2-ketovalerate aldolase—aldehyde dehydrogenase (acylating) from Pseudomonas sp. strain CF600. Acta Crystallogr. D Biol. Crystallogr. 57 (2001) 582–585. [PMID: 11264589]
4.  Baker, P., Carere, J. and Seah, S.Y.K. Probing the molecular basis of substrate specificity, stereospecificity, and catalysis in the class II pyruvate aldolase, BphI. Biochemistry 50 (2011) 3559–3569. [DOI] [PMID: 21425833]
5.  Baker, P., Hillis, C., Carere, J. and Seah, S.Y.K. Protein-protein interactions and substrate channeling in orthologous and chimeric aldolase-dehydrogenase complexes. Biochemistry 51 (2012) 1942–1952. [DOI] [PMID: 22316175]
6.  Baker, P. and Seah, S.Y.K. Rational design of stereoselectivity in the class II pyruvate aldolase BphI. J. Am. Chem. Soc. 134 (2012) 507–513. [DOI] [PMID: 22081904]
[EC 4.1.3.39 created 2006, modified 2011]
 
 
EC 4.1.3.43     
Accepted name: 4-hydroxy-2-oxohexanoate aldolase
Reaction: (S)-4-hydroxy-2-oxohexanoate = propanal + pyruvate
Other name(s): BphI
Systematic name: (S)-4-hydroxy-2-oxohexanoate pyruvate-lyase (propanal-forming)
Comments: Requires Mn2+ for maximal activity [1,2]. The enzymes from the bacteria Burkholderia xenovorans and Thermus thermophilus also perform the reaction of EC 4.1.3.39, 4-hydroxy-2-oxovalerate aldolase [1,2,6]. The enzyme forms a bifunctional complex with EC 1.2.1.87, propanal dehydrogenase (CoA-propanoylating), with a tight channel connecting the two subunits [3,4,6].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Baker, P., Pan, D., Carere, J., Rossi, A., Wang, W. and Seah, S.Y.K. Characterization of an aldolase-dehydrogenase complex that exhibits substrate channeling in the polychlorinated biphenyls degradation pathway. Biochemistry 48 (2009) 6551–6558. [DOI] [PMID: 19476337]
2.  Wang, W., Baker, P. and Seah, S.Y.K. Comparison of two metal-dependent pyruvate aldolases related by convergent evolution: substrate specificity, kinetic mechanism, and substrate channeling. Biochemistry 49 (2010) 3774–3782. [DOI] [PMID: 20364820]
3.  Baker, P., Carere, J. and Seah, S.Y.K. Probing the molecular basis of substrate specificity, stereospecificity, and catalysis in the class II pyruvate aldolase, BphI. Biochemistry 50 (2011) 3559–3569. [DOI] [PMID: 21425833]
4.  Carere, J., Baker, P. and Seah, S.Y.K. Investigating the molecular determinants for substrate channeling in BphI-BphJ, an aldolase-dehydrogenase complex from the polychlorinated biphenyls degradation pathway. Biochemistry 50 (2011) 8407–8416. [DOI] [PMID: 21838275]
5.  Baker, P. and Seah, S.Y.K. Rational design of stereoselectivity in the class II pyruvate aldolase BphI. J. Am. Chem. Soc. 134 (2012) 507–513. [DOI] [PMID: 22081904]
6.  Baker, P., Hillis, C., Carere, J. and Seah, S.Y.K. Protein-protein interactions and substrate channeling in orthologous and chimeric aldolase-dehydrogenase complexes. Biochemistry 51 (2012) 1942–1952. [DOI] [PMID: 22316175]
[EC 4.1.3.43 created 2013]
 
 
EC 4.2.1.132     
Accepted name: 2-hydroxyhexa-2,4-dienoate hydratase
Reaction: 4-hydroxy-2-oxohexanoate = (2Z,4Z)-2-hydroxyhexa-2,4-dienoate + H2O
Other name(s): tesE (gene name); hsaE (gene name)
Systematic name: 4-hydroxy-2-oxohexanoate hydro-lyase [(2Z,4Z)-2-hydroxyhexa-2,4-dienoate-forming]
Comments: This enzyme catalyses a late step in the bacterial steroid degradation pathway. The product, 4-hydroxy-2-oxohexanoate, forms a 2-hydroxy-4-hex-2-enolactone under acidic conditions.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Horinouchi, M., Hayashi, T., Koshino, H., Kurita, T. and Kudo, T. Identification of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid, 4-hydroxy-2-oxohexanoic acid, and 2-hydroxyhexa-2,4-dienoic acid and related enzymes involved in testosterone degradation in Comamonas testosteroni TA441. Appl. Environ. Microbiol. 71 (2005) 5275–5281. [DOI] [PMID: 16151114]
[EC 4.2.1.132 created 2012]
 
 


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