The Enzyme Database

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EC 1.3.8.10     
Accepted name: cyclohex-1-ene-1-carbonyl-CoA dehydrogenase
Reaction: cyclohex-1-ene-1-carbonyl-CoA + electron-transfer flavoprotein = cyclohex-1,5-diene-1-carbonyl-CoA + reduced electron-transfer flavoprotein
Systematic name: cyclohex-1-ene-1-carbonyl-CoA:electron transfer flavoprotein oxidoreductase
Comments: Contains FAD. The enzyme, characterized from the strict anaerobic bacterium Syntrophus aciditrophicus, is involved in production of cyclohexane-1-carboxylate, a byproduct produced by that organism during fermentation of benzoate and crotonate to acetate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kung, J.W., Seifert, J., von Bergen, M. and Boll, M. Cyclohexanecarboxyl-coenzyme A (CoA) and cyclohex-1-ene-1-carboxyl-CoA dehydrogenases, two enzymes involved in the fermentation of benzoate and crotonate in Syntrophus aciditrophicus. J. Bacteriol. 195 (2013) 3193–3200. [DOI] [PMID: 23667239]
[EC 1.3.8.10 created 2013]
 
 
EC 1.3.8.11     
Accepted name: cyclohexane-1-carbonyl-CoA dehydrogenase (electron-transfer flavoprotein)
Reaction: cyclohexane-1-carbonyl-CoA + electron-transfer flavoprotein = cyclohex-1-ene-1-carbonyl-CoA + reduced electron-transfer flavoprotein
Other name(s): aliB (gene name); cyclohexane-1-carbonyl-CoA dehydrogenase (ambiguous)
Systematic name: cyclohexane-1-carbonyl-CoA:electron transfer flavoprotein oxidoreductase
Comments: Contains FAD. The enzyme, characterized from the strict anaerobic bacterium Syntrophus aciditrophicus, is involved in production of cyclohexane-1-carboxylate, a byproduct produced by that organism during fermentation of benzoate and crotonate to acetate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Pelletier, D.A. and Harwood, C.S. 2-Hydroxycyclohexanecarboxyl coenzyme A dehydrogenase, an enzyme characteristic of the anaerobic benzoate degradation pathway used by Rhodopseudomonas palustris. J. Bacteriol. 182 (2000) 2753–2760. [PMID: 10781543]
2.  Kung, J.W., Seifert, J., von Bergen, M. and Boll, M. Cyclohexanecarboxyl-coenzyme A (CoA) and cyclohex-1-ene-1-carboxyl-CoA dehydrogenases, two enzymes involved in the fermentation of benzoate and crotonate in Syntrophus aciditrophicus. J. Bacteriol. 195 (2013) 3193–3200. [DOI] [PMID: 23667239]
[EC 1.3.8.11 created 2013, modified 2020]
 
 
EC 1.3.8.15     
Accepted name: 3-(aryl)acrylate reductase
Reaction: (1) phloretate + electron-transfer flavoprotein = 4-coumarate + reduced electron-transfer flavoprotein
(2) 3-phenylpropanoate + electron-transfer flavoprotein = trans-cinnamate + reduced electron-transfer flavoprotein
(3) 3-(1H-indol-3-yl)propanoate + electron-transfer flavoprotein = 3-(indol-3-yl)acrylate + reduced electron-transfer flavoprotein
Glossary: phloretate = 3-(4-hydroxyphenyl)propanoate
crotonate = (2E)-but-2-enoate
Other name(s): acdA (gene name)
Systematic name: 3-(phenyl)propanoate:electron-transfer flavoprotein 2,3-oxidoreductase
Comments: The enzyme, found in some amino acid-fermenting anaerobic bacteria, participates in the fermentation pathways of L-phenylalanine, L-tyrosine, and L-tryptophan. Unlike EC 1.3.1.31, 2-enoate reductase, this enzyme has minimal activity with crotonate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Dodd, D., Spitzer, M.H., Van Treuren, W., Merrill, B.D., Hryckowian, A.J., Higginbottom, S.K., Le, A., Cowan, T.M., Nolan, G.P., Fischbach, M.A. and Sonnenburg, J.L. A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites. Nature 551 (2017) 648–652. [PMID: 29168502]
[EC 1.3.8.15 created 2019]
 
 
EC 3.7.1.9     
Accepted name: 2-hydroxymuconate-6-semialdehyde hydrolase
Reaction: 2-hydroxymuconate-6-semialdehyde + H2O = formate + 2-oxopent-4-enoate
For diagram of catechol catabolism (meta ring cleavage), click here
Glossary: 2-hydroxymuconate-6-semialdehyde = (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate
Other name(s): 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase; 2-hydroxymuconic semialdehyde hydrolase; HMSH; HOD hydrolase; xylF (gene name); 2-hydroxymuconate-semialdehyde formylhydrolase; 2-hydroxymuconate-semialdehyde hydrolase
Systematic name: 2-hydroxymuconate-6-semialdehyde formylhydrolase
Comments: The enzyme is involved in the degradation of catechols.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD, CAS registry number: 54004-61-4
References:
1.  Sala-Trepat, J.M. and Evans, W.C. The meta cleavage of catechol by Azotobacter species. 4-Oxalocrotonate pathway. Eur. J. Biochem. 20 (1971) 400–413. [DOI] [PMID: 4325686]
2.  Harayama, S., Rekik, M., Wasserfallen, A. and Bairoch, A. Evolutionary relationships between catabolic pathways for aromatics: conservtion of gene order and nucleotide sequences of catechol oxidation genes of pWW0 and NAH7 plasmids. MGG Mol. Gen. Genet. 210 (1987) 241–247. [PMID: 3481421]
3.  Diaz, E. and Timmis, K.N. Identification of functional residues in a 2-hydroxymuconic semialdehyde hydrolase. A new member of the α/β hydrolase-fold family of enzymes which cleaves carbon-carbon bonds. J. Biol. Chem. 270 (1995) 6403–6411. [DOI] [PMID: 7890778]
[EC 3.7.1.9 created 1990, modified 2013]
 
 
EC 4.1.1.77     
Accepted name: 2-oxo-3-hexenedioate decarboxylase
Reaction: (3E)-2-oxohex-3-enedioate = 2-oxopent-4-enoate + CO2
For diagram of catechol catabolism (meta ring cleavage), click here
Other name(s): 4-oxalocrotonate carboxy-lyase (misleading); 4-oxalocrotonate decarboxylase (misleading); cnbF (gene name); praD (gene name); amnE (gene name); nbaG (gene name); xylI (gene name)
Systematic name: (3E)-2-oxohex-3-enedioate carboxy-lyase (2-oxopent-4-enoate-forming)
Comments: Involved in the meta-cleavage pathway for the degradation of phenols, modified phenols and catechols. The enzyme has been reported to accept multiple tautomeric forms [1-4]. However, careful analysis of the stability of the different tautomers, as well as characterization of the enzyme that produces its substrate, EC 5.3.2.6, 2-hydroxymuconate tautomerase, showed that the actual substrate for the enzyme is (3E)-2-oxohex-3-enedioate [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD, CAS registry number: 37325-55-6
References:
1.  Shingler, V., Marklund, U., Powlowski, J. Nucleotide sequence and functional analysis of the complete phenol/3,4-dimethylphenol catabolic pathway of Pseudomonas sp. strain CF600. J. Bacteriol. 174 (1992) 711–724. [DOI] [PMID: 1732207]
2.  Takenaka, S., Murakami, S., Shinke, R. and Aoki, K. Metabolism of 2-aminophenol by Pseudomonas sp. AP-3: modified meta-cleavage pathway. Arch. Microbiol. 170 (1998) 132–137. [PMID: 9683650]
3.  Stanley, T.M., Johnson, W.H., Jr., Burks, E.A., Whitman, C.P., Hwang, C.C. and Cook, P.F. Expression and stereochemical and isotope effect studies of active 4-oxalocrotonate decarboxylase. Biochemistry 39 (2000) 718–726. [DOI] [PMID: 10651637]
4.  Wang, S.C., Johnson, W.H., Jr., Czerwinski, R.M., Stamps, S.L. and Whitman, C.P. Kinetic and stereochemical analysis of YwhB, a 4-oxalocrotonate tautomerase homologue in Bacillus subtilis: mechanistic implications for the YwhB- and 4-oxalocrotonate tautomerase-catalyzed reactions. Biochemistry 46 (2007) 11919–11929. [DOI] [PMID: 17902707]
5.  Kasai, D., Fujinami, T., Abe, T., Mase, K., Katayama, Y., Fukuda, M. and Masai, E. Uncovering the protocatechuate 2,3-cleavage pathway genes. J. Bacteriol. 191 (2009) 6758–6768. [DOI] [PMID: 19717587]
[EC 4.1.1.77 created 1999, modified 2011, modified 2012]
 
 
EC 4.2.1.80     
Accepted name: 2-oxopent-4-enoate hydratase
Reaction: (S)-4-hydroxy-2-oxopentanoate = (2Z)-2-hydroxypenta-2,4-dienoate + H2O
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
Other name(s): 2-keto-4-pentenoate hydratase; OEH; 2-keto-4-pentenoate (vinylpyruvate)hydratase; 4-hydroxy-2-oxopentanoate hydro-lyase; 4-hydroxy-2-oxopentanoate hydro-lyase (2-oxopent-4-enoate-forming); mhpD (gene name); ahdF (gene name); todG (gene name); cmtF (gene name); xylJ (gene name); cnbE (gene name)
Systematic name: (S)-4-hydroxy-2-oxopentanoate hydro-lyase ((2Z)-2-hydroxypenta-2,4-dienoate-forming)
Comments: The enzyme is involved in the catechol meta-cleavage pathway, a major mechanism for degradation of aromatic compounds. Also acts, more slowly, on cis-2-oxohex-4-enoate, but not on the trans-isomer. The enzyme was named when it was thought that the substrate is 2-oxopent-4-enoate. However, it was later found that the actual substrate is its tautomer (2Z)-2-hydroxypenta-2,4-dienoate. In some organisms the enzyme forms a complex with EC 4.1.1.77, 2-oxo-3-hexenedioate decarboxylase (previously named 4-oxalocrotonate decarboxylase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, UM-BBD, CAS registry number: 64427-80-1
References:
1.  Kunz, D.A., Ribbons, D.W. and Chapman, P.J. Metabolism of allylglycine and cis-crotylglycine by Pseudomonas putida (arvilla) mt-2 harboring a TOL plasmid. J. Bacteriol. 148 (1981) 72–82. [PMID: 7287632]
2.  Harayama, S., Rekik, M., Ngai, K.L. and Ornston, L.N. Physically associated enzymes produce and metabolize 2-hydroxy-2,4-dienoate, a chemically unstable intermediate formed in catechol metabolism via meta cleavage in Pseudomonas putida. J. Bacteriol. 171 (1989) 6251–6258. [DOI] [PMID: 2681159]
3.  Pollard, J.R. and Bugg, T.D. Purification, characterisation and reaction mechanism of monofunctional 2-hydroxypentadienoic acid hydratase from Escherichia coli. Eur. J. Biochem. 251 (1998) 98–106. [PMID: 9492273]
[EC 4.2.1.80 created 1984]
 
 
EC 5.3.2.6     
Accepted name: 2-hydroxymuconate tautomerase
Reaction: (2Z,4E)-2-hydroxyhexa-2,4-dienedioate = (3E)-2-oxohex-3-enedioate
For diagram of catechol catabolism (meta ring cleavage), click here
Glossary: (2Z,4E)-2-hydroxyhexa-2,4-dienedioate = (2Z,4E)-2-hydroxymuconate
Other name(s): 4-oxalocrotonate tautomerase (misleading); 4-oxalocrotonate isomerase (misleading); cnbG (gene name); praC (gene name); xylH (gene name)
Systematic name: (2Z,4E)-2-hydroxyhexa-2,4-dienedioate ketoenol isomerase
Comments: Involved in the meta-cleavage pathway for the degradation of phenols, modified phenols and catechols. The enol form (2Z,4E)-2-hydroxyhexa-2,4-dienedioate is produced as part of this pathway and is converted to the keto form (3E)-2-oxohex-3-enedioate by the enzyme [6]. Another keto form, (4E)-2-oxohex-4-enedioate (4-oxalocrotonate), was originally thought to be produced by the enzyme [1,2] but later shown to be produced non-enzymically [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Whitman, C.P., Aird, B.A., Gillespie, W.R. and Stolowich, N.J. Chemical and enzymatic ketonization of 2-hydroxymuconate, a conjugated enol. J. Am. Chem. Soc. 113 (1991) 3154–3162.
2.  Whitman, C.P., Hajipour, G., Watson, R.J., Johnson, W.H., Jr., Bembenek, M.E. and Stolowich, N.J. Stereospecific ketonization of 2-hydroxymuconate by 4-oxalocrotonate tautomerase and 5-(carboxymethyl)-2-hydroxymuconate isomerase. J. Am. Chem. Soc. 114 (1992) 10104–10110.
3.  Subramanya, H.S., Roper, D.I., Dauter, Z., Dodson, E.J., Davies, G.J., Wilson, K.S. and Wigley, D.B. Enzymatic ketonization of 2-hydroxymuconate: specificity and mechanism investigated by the crystal structures of two isomerases. Biochemistry 35 (1996) 792–802. [DOI] [PMID: 8547259]
4.  Stivers, J.T., Abeygunawardana, C., Mildvan, A.S., Hajipour, G., Whitman, C.P. and Chen, L.H. Catalytic role of the amino-terminal proline in 4-oxalocrotonate tautomerase: affinity labeling and heteronuclear NMR studies. Biochemistry 35 (1996) 803–813. [DOI] [PMID: 8547260]
5.  Wang, S.C., Johnson, W.H., Jr., Czerwinski, R.M., Stamps, S.L. and Whitman, C.P. Kinetic and stereochemical analysis of YwhB, a 4-oxalocrotonate tautomerase homologue in Bacillus subtilis: mechanistic implications for the YwhB- and 4-oxalocrotonate tautomerase-catalyzed reactions. Biochemistry 46 (2007) 11919–11929. [DOI] [PMID: 17902707]
6.  Kasai, D., Fujinami, T., Abe, T., Mase, K., Katayama, Y., Fukuda, M. and Masai, E. Uncovering the protocatechuate 2,3-cleavage pathway genes. J. Bacteriol. 191 (2009) 6758–6768. [DOI] [PMID: 19717587]
[EC 5.3.2.6 created 2012]
 
 


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