The Enzyme Database

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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 1.13.11.22     
Accepted name: caffeate 3,4-dioxygenase
Reaction: 3,4-dihydroxy-trans-cinnamate + O2 = 3-(2-carboxyethenyl)-cis,cis-muconate
Other name(s): 3,4-dihydroxy-trans-cinnamate:oxygen 3,4-oxidoreductase (decyclizing)
Systematic name: 3,4-dihydroxy-trans-cinnamate:oxygen 3,4-oxidoreductase (ring-opening)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37256-61-4
References:
1.  Seidman, M.M., Toms, A. and Wood, J.M. Influence of side-chain substituents on the position of cleavage of the benzene ring by Pseudomonas fluorescens. J. Bacteriol. 97 (1969) 1192–1197. [PMID: 5776526]
[EC 1.13.11.22 created 1972]
 
 
EC 1.14.12.19     
Accepted name: 3-phenylpropanoate dioxygenase
Reaction: (1) 3-phenylpropanoate + NADH + H+ + O2 = 3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl)propanoate + NAD+
(2) (2E)-3-phenylprop-2-enoate + NADH + H+ + O2 = (2E)-3-(2,3-dihydroxyphenyl)prop-2-enoate + NAD+
For diagram of reaction, click here
Glossary: (2E)-3-phenylprop-2-enoate = trans-cinnamate
(2E)-3-(2,3-dihydroxyphenyl)prop-2-enoate = trans-2,3-dihydroxycinnamate
Other name(s): HcaA1A2CD; Hca dioxygenase; 3-phenylpropionate dioxygenase
Systematic name: 3-phenylpropanoate,NADH:oxygen oxidoreductase (2,3-hydroxylating)
Comments: This enzyme catalyses a step in the pathway of phenylpropanoid compounds degradation. It catalyses the insertion of both atoms of molecular oxygen into positions 2 and 3 of the phenyl ring of 3-phenylpropanoate or (2E)-3-phenylprop-2-enoate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD
References:
1.  Díaz, E., Ferrández, A. and García, J.L. Characterization of the hca cluster encoding the dioxygenolytic pathway for initial catabolism of 3-phenylpropionic acid in Escherichia coli K-12. J. Bacteriol. 180 (1998) 2915–2923. [PMID: 9603882]
2.  Burlingame, R. and Chapman, P.J. Catabolism of phenylpropionic acid and its 3-hydroxy derivative by Escherichia coli. J. Bacteriol. 155 (1983) 113–121. [PMID: 6345502]
[EC 1.14.12.19 created 2005, modified 2011]
 
 
EC 1.14.13.11      
Transferred entry: trans-cinnamate 4-monooxygenase. Now EC 1.14.14.91, trans-cinnamate 4-monooxygenase
[EC 1.14.13.11 created 1976, deleted 2018]
 
 
EC 1.14.13.14     
Accepted name: trans-cinnamate 2-monooxygenase
Reaction: trans-cinnamate + NADPH + H+ + O2 = 2-hydroxycinnamate + NADP+ + H2O
Other name(s): cinnamic acid 2-hydroxylase; cinnamate 2-monooxygenase; cinnamic 2-hydroxylase; cinnamate 2-hydroxylase; trans-cinnamic acid 2-hydroxylase
Systematic name: trans-cinnamate,NADPH:oxygen oxidoreductase (2-hydroxylating)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 53126-56-0
References:
1.  Gestetner, B. and Conn, E.E. The 2-hydroxylation of trans-cinnamic acid by chloroplasts from Melilotus alba Desr. Arch. Biochem. Biophys. 163 (1974) 617–624. [DOI] [PMID: 4153528]
[EC 1.14.13.14 created 1976]
 
 
EC 1.14.14.91     
Accepted name: trans-cinnamate 4-monooxygenase
Reaction: trans-cinnamate + [reduced NADPH—hemoprotein reductase] + O2 = 4-hydroxycinnamate + [oxidized NADPH—hemoprotein reductase] + H2O
For diagram of chalcone and stilbene biosynthesis, click here
Other name(s): cinnamic acid 4-hydroxylase; CA4H; cytochrome P450 cinnamate 4-hydroxylase; cinnamate 4-hydroxylase; cinnamate 4-monooxygenase; cinnamate hydroxylase; cinnamic 4-hydroxylase; cinnamic acid 4-monooxygenase; cinnamic acid p-hydroxylase; t-cinnamic acid hydroxylase; trans-cinnamate 4-hydroxylase; trans-cinnamic acid 4-hydroxylase; CYP73A1 (gene name)
Systematic name: trans-cinnamate,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (4-hydroxylating)
Comments: A cytochrome P-450 (heme-thiolate) protein found in plants. The enzyme is involved in flavonoid biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9077-75-2
References:
1.  Potts, J.R.M., Weklych, R. and Conn, E.E. The 4-hydroxylation of cinnamic acid by sorghum microsomes and the requirement for cytochrome P-450. J. Biol. Chem. 249 (1974) 5019–5026. [PMID: 4153152]
2.  Russell, D.W. and Conn, E.E. The cinnamic acid 4-hydroxylase of pea seedlings. Arch. Biochem. Biophys. 122 (1967) 256–268. [DOI] [PMID: 4383827]
3.  Pierrel, M.A., Batard, Y., Kazmaier, M., Mignotte-Vieux, C., Durst, F. and Werck-Reichhart, D. Catalytic properties of the plant cytochrome P450 CYP73 expressed in yeast. Substrate specificity of a cinnamate hydroxylase. Eur. J. Biochem. 224 (1994) 835–844. [PMID: 7925408]
[EC 1.14.14.91 created 1976 as EC 1.14.13.11, transferred 2018 to EC 1.14.14.91]
 
 
EC 2.1.1.68     
Accepted name: caffeate O-methyltransferase
Reaction: S-adenosyl-L-methionine + 3,4-dihydroxy-trans-cinnamate = S-adenosyl-L-homocysteine + 3-methoxy-4-hydroxy-trans-cinnamate
Other name(s): caffeate methyltransferase; caffeate 3-O-methyltransferase; S-adenosyl-L-methionine:caffeic acid-O-methyltransferase
Systematic name: S-adenosyl-L-methionine:3,4-dihydroxy-trans-cinnamate 3-O-methyltransferase
Comments: 3,4-Dihydroxybenzaldehyde and catechol can act as acceptors, but more slowly.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 50936-45-3
References:
1.  Ebel, J., Schaller-Hekeler, B., Knobloch, K.-H., Wellman, E., Grisebach, H. and Hahlbrock, K. Coordinated changes in enzyme activities of phenylpropanoid metabolism during the growth of soybean cell suspension cultures. Biochim. Biophys. Acta 362 (1974) 417–424. [DOI] [PMID: 4472044]
2.  Poulton, J.E. and Butt, V.S. Purification and properties of S-adenosyl-L-methionine: caffeic acid O-methyltransferase from leaves of spinach beet (Beta vulgaris L). Biochim. Biophys. Acta 403 (1975) 301–314. [DOI] [PMID: 241400]
3.  Shimada, M., Kuroda, H. and Higuchi, T. Evidence for the formation of methoxyl groups of ferulic and sinapic acid in Bambusa by the same O-methyltransferase. Phytochemistry 12 (1973) 2873–2875.
[EC 2.1.1.68 created 1984]
 
 
EC 2.4.1.177     
Accepted name: cinnamate β-D-glucosyltransferase
Reaction: UDP-glucose + trans-cinnamate = UDP + trans-cinnamoyl β-D-glucoside
Other name(s): uridine diphosphoglucose-cinnamate glucosyltransferase; UDPG:t-cinnamate glucosyltransferase
Systematic name: UDP-glucose:trans-cinnamate β-D-glucosyltransferase
Comments: 4-Coumarate, 2-coumarate, benzoate, feruloate and caffeate can also act as acceptors, but more slowly. Involved in the biosynthesis of chlorogenic acid in the root of the sweet potato, Ipomoea batatas.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 83744-95-0
References:
1.  Shimizu, T. and Kojima, M. Partial purification and characterization of UDPG:t-cinnamate glucosyltransferase in the root of sweet potato, Ipomoea batatas Lam. J. Biochem. (Tokyo) 95 (1984) 205–213. [PMID: 6231280]
[EC 2.4.1.177 created 1989]
 
 
EC 4.1.1.102     
Accepted name: phenacrylate decarboxylase
Reaction: (1) 4-coumarate = 4-vinylphenol + CO2
(2) trans-cinnamate = styrene + CO2
(3) ferulate = 4-vinylguaiacol + CO2
Glossary: 4-coumarate = 3-(4-hydroxyphenyl)prop-2-enoate
trans-cinnamate = (2E)-3-phenylprop-2-enoate
ferulate = 4-hydroxy-3-methoxycinnamate
Other name(s): FDC1 (gene name); ferulic acid decarboxylase
Systematic name: 3-phenylprop-2-enoate carboxy-lyase
Comments: The enzyme, found in fungi, catalyses the decarboxylation of phenacrylic acids present in plant cell walls. It requires a prenylated flavin cofactor that is produced by EC 2.5.1.129, flavin prenyltransferase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Mukai, N., Masaki, K., Fujii, T., Kawamukai, M. and Iefuji, H. PAD1 and FDC1 are essential for the decarboxylation of phenylacrylic acids in Saccharomyces cerevisiae. J. Biosci. Bioeng. 109 (2010) 564–569. [DOI] [PMID: 20471595]
2.  Bhuiya, M.W., Lee, S.G., Jez, J.M. and Yu, O. Structure and mechanism of ferulic acid decarboxylase (FDC1) from Saccharomyces cerevisiae. Appl. Environ. Microbiol. 81 (2015) 4216–4223. [DOI] [PMID: 25862228]
3.  Payne, K.A., White, M.D., Fisher, K., Khara, B., Bailey, S.S., Parker, D., Rattray, N.J., Trivedi, D.K., Goodacre, R., Beveridge, R., Barran, P., Rigby, S.E., Scrutton, N.S., Hay, S. and Leys, D. New cofactor supports α,β-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition. Nature 522 (2015) 497–501. [DOI] [PMID: 26083754]
[EC 4.1.1.102 created 2015]
 
 
EC 4.3.1.5      
Transferred entry: phenylalanine ammonia-lyase. Now divided into EC 4.3.1.23 (tyrosine ammonia-lyase), EC 4.3.1.24 (phenylalanine ammonia-lyase) and EC 4.3.1.25 (phenylalanine/tyrosine ammonia-lyase)
[EC 4.3.1.5 created 1965, deleted 2008]
 
 
EC 4.3.1.24     
Accepted name: phenylalanine ammonia-lyase
Reaction: L-phenylalanine = trans-cinnamate + NH3
For diagram of chalcone and stilbene biosynthesis, click here
Other name(s): phenylalanine deaminase; phenylalanine ammonium-lyase; PAL; L-phenylalanine ammonia-lyase; Phe ammonia-lyase
Systematic name: L-phenylalanine ammonia-lyase (trans-cinnamate-forming)
Comments: This enzyme is a member of the aromatic amino acid lyase family, other members of which are EC 4.3.1.3 (histidine ammonia-lyase) and EC 4.3.1.23 (tyrosine ammonia-lyase) and EC 4.3.1.25 (phenylalanine/tyrosine ammonia-lyase). The enzyme contains the cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO), which is common to this family [3]. This unique cofactor is formed autocatalytically by cyclization and dehydration of the three amino-acid residues alanine, serine and glycine [9]. The enzyme from some species is highly specific for phenylalanine [7,8].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9024-28-6
References:
1.  Koukol, J. and Conn, E.E. The metabolism of aromatic compounds in higher plants. IV. Purification and properties of the phenylalanine deaminase of Hordeum vulgare. J. Biol. Chem. 236 (1961) 2692–2698. [PMID: 14458851]
2.  Young, M.R. and Neish, A.C. Properties of the ammonia-lyases deaminating phenylalanine and related compounds in Triticum sestivum and Pteridium aquilinum. Phytochemistry 5 (1966) 1121–1132.
3.  Louie, G.V., Bowman, M.E., Moffitt, M.C., Baiga, T.J., Moore, B.S. and Noel, J.P. Structural determinants and modulation of substrate specificity in phenylalanine-tyrosine ammonia-lyases. Chem. Biol. 13 (2006) 1327–1338. [DOI] [PMID: 17185228]
4.  Calabrese, J.C., Jordan, D.B., Boodhoo, A., Sariaslani, S. and Vannelli, T. Crystal structure of phenylalanine ammonia lyase: multiple helix dipoles implicated in catalysis. Biochemistry 43 (2004) 11403–11416. [DOI] [PMID: 15350127]
5.  Ritter, H. and Schulz, G.E. Structural basis for the entrance into the phenylpropanoid metabolism catalyzed by phenylalanine ammonia-lyase. Plant Cell 16 (2004) 3426–3436. [DOI] [PMID: 15548745]
6.  Watts, K.T., Mijts, B.N., Lee, P.C., Manning, A.J. and Schmidt-Dannert, C. Discovery of a substrate selectivity switch in tyrosine ammonia-lyase, a member of the aromatic amino acid lyase family. Chem. Biol. 13 (2006) 1317–1326. [DOI] [PMID: 17185227]
7.  Appert, C., Logemann, E., Hahlbrock, K., Schmid, J. and Amrhein, N. Structural and catalytic properties of the four phenylalanine ammonia-lyase isoenzymes from parsley (Petroselinum crispum Nym.). Eur. J. Biochem. 225 (1994) 491–499. [DOI] [PMID: 7925471]
8.  Cochrane, F.C., Davin, L.B. and Lewis, N.G. The Arabidopsis phenylalanine ammonia lyase gene family: kinetic characterization of the four PAL isoforms. Phytochemistry 65 (2004) 1557–1564. [DOI] [PMID: 15276452]
9.  Schwede, T.F., Rétey, J. and Schulz, G.E. Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile. Biochemistry 38 (1999) 5355–5361. [DOI] [PMID: 10220322]
[EC 4.3.1.24 created 2008 (EC 4.3.1.5 created 1965, part-incorporated 2008)]
 
 
EC 4.3.1.25     
Accepted name: phenylalanine/tyrosine ammonia-lyase
Reaction: (1) L-phenylalanine = trans-cinnamate + NH3
(2) L-tyrosine = trans-p-hydroxycinnamate + NH3
For diagram of chalcone and stilbene biosynthesis, click here
Other name(s): PTAL; bifunctional PAL
Systematic name: L-phenylalanine(or L-tyrosine):trans-cinnamate(or trans-p-hydroxycinnamate) ammonia-lyase
Comments: This enzyme is a member of the aromatic amino acid lyase family, other members of which are EC 4.3.1.3 (histidine ammonia-lyase), EC 4.3.1.23 (tyrosine ammonia-lyase) and EC 4.3.1.24 (phenylalanine ammonia-lyase). The enzyme from some monocots, including maize, and from the yeast Rhodosporidium toruloides, deaminate L-phenylalanine and L-tyrosine with similar catalytic efficiency [3]. The enzyme contains the cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO), which is common to this family [3]. This unique cofactor is formed autocatalytically by cyclization and dehydration of the three amino-acid residues alanine, serine and glycine [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Rösler, J., Krekel, F., Amrhein, N. and Schmid, J. Maize phenylalanine ammonia-lyase has tyrosine ammonia-lyase activity. Plant Physiol. 113 (1997) 175–179. [PMID: 9008393]
2.  Watts, K.T., Mijts, B.N., Lee, P.C., Manning, A.J. and Schmidt-Dannert, C. Discovery of a substrate selectivity switch in tyrosine ammonia-lyase, a member of the aromatic amino acid lyase family. Chem. Biol. 13 (2006) 1317–1326. [DOI] [PMID: 17185227]
3.  Louie, G.V., Bowman, M.E., Moffitt, M.C., Baiga, T.J., Moore, B.S. and Noel, J.P. Structural determinants and modulation of substrate specificity in phenylalanine-tyrosine ammonia-lyases. Chem. Biol. 13 (2006) 1327–1338. [DOI] [PMID: 17185228]
4.  Schwede, T.F., Rétey, J. and Schulz, G.E. Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile. Biochemistry 38 (1999) 5355–5361. [DOI] [PMID: 10220322]
[EC 4.3.1.25 created 2008 (EC 4.3.1.5 created 1965, part-incorporated 2008)]
 
 


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