The Enzyme Database

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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 1.2.1.27     
Accepted name: methylmalonate-semialdehyde dehydrogenase (CoA-acylating)
Reaction: 2-methyl-3-oxopropanoate + CoA + H2O + NAD+ = propanoyl-CoA + HCO3- + NADH
For diagram of inositol catabolism, click here
Glossary: methylmalonate semialdehyde = 2-methyl-3-oxopropanoate
Other name(s): MSDH; MMSA dehydrogenase; iolA (gene name); methylmalonate-semialdehyde dehydrogenase (acylating)
Systematic name: 2-methyl-3-oxopropanoate:NAD+ 3-oxidoreductase (CoA-propanoylating)
Comments: Also converts 3-oxopropanoate into acetyl-CoA [3]. The reaction occurs in two steps with the decarboxylation process preceding CoA-binding [3]. Bicarbonate rather than CO2 is released as a final product [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37205-49-5
References:
1.  Sokatch, J.R., Sanders, L.E. and Marshall, V.P. Oxidation of methylmalonate semialdehyde to propionyl coenzyme A in Pseudomonas aeruginosa grown on valine. J. Biol. Chem. 243 (1968) 2500–2506. [PMID: 4297649]
2.  Dubourg, H., Stines-Chaumeil, C., Didierjean, C., Talfournier, F., Rahuel-Clermont, S., Branlant, G. and Aubry, A. Expression, purification, crystallization and preliminary X-ray diffraction data of methylmalonate-semialdehyde dehydrogenase from Bacillus subtilis. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 1435–1437. [DOI] [PMID: 15272169]
3.  Stines-Chaumeil, C., Talfournier, F. and Branlant, G. Mechanistic characterization of the MSDH (methylmalonate semialdehyde dehydrogenase) from Bacillus subtilis. Biochem. J. 395 (2006) 107–115. [DOI] [PMID: 16332250]
[EC 1.2.1.27 created 1972, modified 2014]
 
 
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
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 1.2.7.2      
Deleted entry: 2-oxobutyrate synthase. Now included with EC 1.2.7.1, pyruvate synthase.
[EC 1.2.7.2 created 1972, deleted 2013]
 
 
EC 1.3.1.84     
Accepted name: acrylyl-CoA reductase (NADPH)
Reaction: propanoyl-CoA + NADP+ = acryloyl-CoA + NADPH + H+
For diagram of the 3-hydroxypropanoate cycle, click here, for diagram of the 3-hydroxypropanoate/4-hydroxybutanoate cycle and dicarboxylate/4-hydroxybutanoate cycle in archaea, click here and for diagram of 3-(dimethylsulfonio)propanoate met
Glossary: propanoyl-CoA = propionyl-CoA
acryloyl-CoA = acrylyl-CoA = propenoyl-CoA
Systematic name: propanoyl-CoA:NADP+ oxidoreductase
Comments: Catalyses a step in the 3-hydroxypropanoate/4-hydroxybutanoate cycle, an autotrophic CO2 fixation pathway found in some thermoacidophilic archaea [1]. The enzyme from Sulfolobus tokodaii does not act on either NADH or crotonyl-CoA [2]. Different from EC 1.3.1.8, which acts only on enoyl-CoA derivatives of carbon chain length 4 to 16. Contains Zn2+.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Berg, I.A., Kockelkorn, D., Buckel, W. and Fuchs, G. A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea. Science 318 (2007) 1782–1786. [DOI] [PMID: 18079405]
2.  Teufel, R., Kung, J.W., Kockelkorn, D., Alber, B.E. and Fuchs, G. 3-hydroxypropionyl-coenzyme A dehydratase and acryloyl-coenzyme A reductase, enzymes of the autotrophic 3-hydroxypropionate/4-hydroxybutyrate cycle in the Sulfolobales. J. Bacteriol. 191 (2009) 4572–4581. [DOI] [PMID: 19429610]
[EC 1.3.1.84 created 2009, modified 2014]
 
 
EC 1.3.1.95     
Accepted name: acrylyl-CoA reductase (NADH)
Reaction: propanoyl-CoA + NAD+ = acryloyl-CoA + NADH + H+
For diagram of 3-(dimethylsulfonio)propanoate metabolism, click here
Glossary: propanoyl-CoA = propionyl-CoA
Systematic name: propanoyl-CoA:NAD+ oxidoreductase
Comments: Contains FAD. The reaction is catalysed in the opposite direction to that shown. The enzyme from the bacterium Clostridium propionicum is a complex that includes an electron-transfer flavoprotein (ETF). The ETF is reduced by NADH and transfers the electrons to the active site. Catalyses a step in a pathway for L-alanine fermentation to propanoate [1]. cf. EC 1.3.1.84, acrylyl-CoA reductase (NADPH).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hetzel, M., Brock, M., Selmer, T., Pierik, A.J., Golding, B.T. and Buckel, W. Acryloyl-CoA reductase from Clostridium propionicum. An enzyme complex of propionyl-CoA dehydrogenase and electron-transferring flavoprotein. Eur. J. Biochem. 270 (2003) 902–910. [DOI] [PMID: 12603323]
2.  Kandasamy, V., Vaidyanathan, H., Djurdjevic, I., Jayamani, E., Ramachandran, K.B., Buckel, W., Jayaraman, G. and Ramalingam, S. Engineering Escherichia coli with acrylate pathway genes for propionic acid synthesis and its impact on mixed-acid fermentation. Appl. Microbiol. Biotechnol. 97 (2013) 1191–1200. [DOI] [PMID: 22810300]
[EC 1.3.1.95 created 2012]
 
 
EC 1.3.1.108     
Accepted name: caffeoyl-CoA reductase
Reaction: 3-(3,4-dihydroxyphenyl)propanoyl-CoA + 2 NAD+ + 2 reduced ferredoxin [iron-sulfur] cluster = (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl-CoA + 2 NADH + 2 oxidized ferredoxin [iron-sulfur] cluster
Glossary: (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl-CoA = (2E)-3-(3,4-dihydroxyphenyl)acryloyl-CoA = trans-caffeoyl-CoA
3-(3,4-dihydroxyphenyl)propanoyl-CoA = hydrocaffeoyl-CoA
Other name(s): electron-bifurcating caffeoyl-CoA reductase; caffeoyl-CoA reductase-Etf complex; hydrocaffeoyl-CoA:NAD+,ferredoxin oxidoreductase
Systematic name: 3-(3,4-dihydroxyphenyl)propanoyl-CoA:NAD+,ferredoxin oxidoreductase
Comments: The enzyme, characterized from the bacterium Acetobacterium woodii, contains two [4Fe-4S] clusters and FAD. The enzyme couples the endergonic ferredoxin reduction with NADH as reductant to the exergonic reduction of caffeoyl-CoA with the same reductant. It uses the mechanism of electron bifurcation to overcome the steep energy barrier in ferredoxin reduction. It also reduces 4-coumaroyl-CoA and feruloyl-CoA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Bertsch, J., Parthasarathy, A., Buckel, W. and Muller, V. An electron-bifurcating caffeyl-CoA reductase. J. Biol. Chem. 288 (2013) 11304–11311. [DOI] [PMID: 23479729]
[EC 1.3.1.108 created 2015]
 
 
EC 1.3.1.117     
Accepted name: hydroxycinnamoyl-CoA reductase
Reaction: (1) dihydro-4-coumaroyl-CoA + NADP+ = trans-4-coumaroyl-CoA + NADPH + H+
(2) dihydroferuloyl-CoA + NADP+ = trans-feruloyl-CoA + NADPH + H+
For diagram of phloretin biosynthesis, click here
Glossary: trans-4-coumaroyl-CoA = (E)-3-(4-hydroxyphenyl)prop-2-enoyl-CoA
trans-feruloyl-CoA = (E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoyl-CoA
dihydro-4-coumaroyl-CoA = 3-(4-hydroxyphenyl)propanoyl-CoA
dihydroferuloyl-CoA = 3-(4-hydroxy-3-methoxyphenyl)propanoyl-CoA
Other name(s): MdHCDBR; hydroxycinnamoyl-CoA double bond reductase
Systematic name: dihydro-4-coumaroyl-CoA:NADP+ 2,3-oxidoreductase
Comments: Isolated from Malus X domestica (apple). Involved in dihydrochalcone biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Ibdah, M., Berim, A., Martens, S., Valderrama, A.L.H., Palmieri, L., Lewinsohn, E. and Gang, D.R. Identification and cloning of an NADPH-dependant hydroxycinnamoyl-CoA double bond reductase involved in dihydrochalcone formation in Malus X domestica Borkh. Phytochemistry 107 (2014) 24-31. [DOI] [PMID: 25152451]
[EC 1.3.1.117 created 2018]
 
 
EC 1.3.99.12      
Transferred entry: 2-methylacyl-CoA dehydrogenase. Now classified as EC 1.3.8.5, 2-methyl-branched-chain-enoyl-CoA reductase.
[EC 1.3.99.12 created 1986, deleted 2020]
 
 
EC 1.17.5.1     
Accepted name: phenylacetyl-CoA dehydrogenase
Reaction: phenylacetyl-CoA + H2O + 2 quinone = phenylglyoxylyl-CoA + 2 quinol
For diagram of phenylacetyl-CoA metabolism, click here
Other name(s): phenylacetyl-CoA:acceptor oxidoreductase
Systematic name: phenylacetyl-CoA:quinone oxidoreductase
Comments: The enzyme from Thauera aromatica is a membrane-bound molybdenum—iron—sulfur protein. The enzyme is specific for phenylacetyl-CoA as substrate. Phenylacetate, acetyl-CoA, benzoyl-CoA, propanoyl-CoA, crotonyl-CoA, succinyl-CoA and 3-hydroxybenzoyl-CoA cannot act as substrates. The oxygen atom introduced into the product, phenylglyoxylyl-CoA, is derived from water and not molecular oxygen. Duroquinone, menaquinone and 2,6-dichlorophenolindophenol (DCPIP) can act as acceptor, but the likely physiological acceptor is ubiquinone [1]. A second enzyme, EC 3.1.2.25, phenylacetyl-CoA hydrolase, converts the phenylglyoxylyl-CoA formed into phenylglyoxylate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 210756-43-7
References:
1.  Rhee, S.K. and Fuchs, G. Phenylacetyl-CoA:acceptor oxidoreductase, a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. Eur. J. Biochem. 262 (1999) 507–515. [DOI] [PMID: 10336636]
2.  Schneider, S. and Fuchs, G. Phenylacetyl-CoA:acceptor oxidoreductase, a new α-oxidizing enzyme that produces phenylglyoxylate. Assay, membrane localization, and differential production in Thauera aromatica. Arch. Microbiol. 169 (1998) 509–516. [PMID: 9575237]
[EC 1.17.5.1 created 2004]
 
 
EC 2.1.3.1     
Accepted name: methylmalonyl-CoA carboxytransferase
Reaction: (S)-methylmalonyl-CoA + pyruvate = propanoyl-CoA + oxaloacetate
Other name(s): transcarboxylase; methylmalonyl coenzyme A carboxyltransferase; methylmalonyl-CoA transcarboxylase; oxalacetic transcarboxylase; methylmalonyl-CoA carboxyltransferase; (S)-2-methyl-3-oxopropanoyl-CoA:pyruvate carboxyltransferase; (S)-2-methyl-3-oxopropanoyl-CoA:pyruvate carboxytransferase carboxytransferase [incorrect]
Systematic name: (S)-methylmalonyl-CoA:pyruvate carboxytransferase
Comments: A biotinyl-protein, containing cobalt and zinc. The enzyme, described from the bacterium Propionibacterium shermanii, is unique among the biotin-dependent enzymes in that it catalyses carboxyl transfer between two organic molecules, utilizing two separate carboxyltransferase domains. The enzyme is a very large complex, consisting of a hexameric central core of 12S subunits surrounded by six 5S subunit dimers, each connected to the central core by twelve 1.3S biotin carrier subunits.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, UM-BBD, CAS registry number: 9029-86-1
References:
1.  Swick, R.W. and Wood, H.G. The role of transcarboxylation in propionic acid fermentation. Proc. Natl. Acad. Sci. USA 46 (1960) 28–41. [DOI] [PMID: 16590594]
2.  Wood, H.G. and Kumar, G.K. Transcarboxylase: its quaternary structure and the role of the biotinyl subunit in the assembly of the enzyme and in catalysis. Ann. N.Y. Acad. Sci. 447 (1985) 1–22. [DOI] [PMID: 3893281]
3.  Peikert, C., Seeger, K., Bhat, R.K. and Berger, S. Determination of the binding specificity of the 12S subunit of the transcarboxylase by saturation transfer difference NMR. Org. Biomol. Chem. 2 (2004) 1777–1781. [DOI] [PMID: 15188046]
4.  Kumar Bhat, R. and Berger, S. New and easy strategy for cloning, expression, purification, and characterization of the 5S subunit of transcarboxylase from Propionibacterium f. shermanii. Prep. Biochem. Biotechnol. 37 (2007) 13–26. [DOI] [PMID: 17134979]
5.  Carey, P.R., Sonnichsen, F.D. and Yee, V.C. Transcarboxylase: one of nature’s early nanomachines. IUBMB Life 56 (2004) 575–583. [DOI] [PMID: 15814455]
[EC 2.1.3.1 created 1961]
 
 
EC 2.3.1.2     
Accepted name: imidazole N-acetyltransferase
Reaction: acetyl-CoA + imidazole = CoA + N-acetylimidazole
Other name(s): imidazole acetylase; imidazole acetyltransferase
Systematic name: acetyl-CoA:imidazole N-acetyltransferase
Comments: Also acts with propanoyl-CoA.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 9029-89-4
References:
1.  Kinsky, S.C. Assay, purification, and properties of imidazole acetylase. J. Biol. Chem. 235 (1960) 94–98. [PMID: 14409246]
[EC 2.3.1.2 created 1961]
 
 
EC 2.3.1.6     
Accepted name: choline O-acetyltransferase
Reaction: acetyl-CoA + choline = CoA + O-acetylcholine
Other name(s): choline acetylase; choline acetyltransferase
Systematic name: acetyl-CoA:choline O-acetyltransferase
Comments: Propanoyl-CoA can act, more slowly, in place of acetyl-CoA.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9012-78-6
References:
1.  Berman, R., Wilson, I.B. and Nachmansohn, D. Choline acetylase specificity in relation to biological function. Biochim. Biophys. Acta 12 (1953) 315–324. [DOI] [PMID: 13115440]
2.  Berry, J.F. and Whittaker, V.P. The acyl-group specificity of choline acetylase. Biochem. J. 73 (1959) 447–458. [PMID: 13799882]
3.  Fritz, I.B. and Schultz, S.K. Carnitine acetyltransferase. II. Inhibition by carnitine analogues and by sulfhydryl reagents. J. Biol. Chem. 240 (1965) 2188–2192. [PMID: 14299645]
4.  Schuberth, J. Choline acetyltransferase. Purification and effect of salts on the mechanism of the enzyme-catalysed reaction. Biochim. Biophys. Acta 122 (1966) 470–481.
[EC 2.3.1.6 created 1961]
 
 
EC 2.3.1.7     
Accepted name: carnitine O-acetyltransferase
Reaction: acetyl-CoA + carnitine = CoA + O-acetylcarnitine
Other name(s): acetyl-CoA-carnitine O-acetyltransferase; acetylcarnitine transferase; carnitine acetyl coenzyme A transferase; carnitine acetylase; carnitine acetyltransferase; carnitine-acetyl-CoA transferase; CATC
Systematic name: acetyl-CoA:carnitine O-acetyltransferase
Comments: Also acts on propanoyl-CoA and butanoyl-CoA (cf. EC 2.3.1.21 carnitine O-palmitoyltransferase and EC 2.3.1.137 carnitine O-octanoyltransferase).
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9029-90-7
References:
1.  Chase, J.F.A., Pearson, D.J. and Tubbs, P.K. The preparation of crystalline carnitine acetyltransferase. Biochim. Biophys. Acta 96 (1965) 162–165. [DOI] [PMID: 14285260]
2.  Friedman, S. and Fraenkel, G. Reversible enzymatic acetylation of carnitine. Arch. Biochem. Biophys. 59 (1955) 491–501. [DOI] [PMID: 13275966]
3.  Miyazawa, S., Ozasa, H., Furuta, S., Osumi, T. and Hashimoto, T. Purification and properties of carnitine acetyl transferase from rat liver. J. Biochem. (Tokyo) 93 (1983) 439–451. [PMID: 6404901]
[EC 2.3.1.7 created 1961]
 
 
EC 2.3.1.66     
Accepted name: leucine N-acetyltransferase
Reaction: acetyl-CoA + L-leucine = CoA + N-acetyl-L-leucine
Other name(s): leucine acetyltransferase
Systematic name: acetyl-CoA:L-leucine N-acetyltransferase
Comments: Propanoyl-CoA can act as a donor, but more slowly. L-Arginine, L-valine, L-phenylalanine and peptides containing L-leucine can act as acceptors.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 75496-56-9
References:
1.  Suzukake, S., Hayashi, H., Hori, M. and Umezawa, H. Biosnthesis of leupeptin III. Isolation and properties of an enzyme synthesizing acetyl-L-leucine. J. Antibiot. 33 (1982) 857–862.
[EC 2.3.1.66 created 1983]
 
 
EC 2.3.1.94     
Accepted name: 6-deoxyerythronolide-B synthase
Reaction: propanoyl-CoA + 6 (2S)-methylmalonyl-CoA + 6 NADPH + 6 H+ = 6-deoxyerythronolide B + 7 CoA + 6 CO2 + H2O + 6 NADP+
For diagram of reaction, click here
Other name(s): erythronolide condensing enzyme; malonyl-CoA:propionyl-CoA malonyltransferase (cyclizing); erythronolide synthase; malonyl-CoA:propanoyl-CoA malonyltransferase (cyclizing); deoxyerythronolide B synthase; 6-deoxyerythronolide B synthase; DEBS
Systematic name: propanoyl-CoA:(2S)-methylmalonyl-CoA malonyltransferase (cyclizing)
Comments: The product, 6-deoxyerythronolide B, contains a 14-membered lactone ring and is an intermediate in the biosynthesis of erythromycin antibiotics. Biosynthesis of 6-deoxyerythronolide B requires 28 active sites that are precisely arranged along three large polypeptides, denoted DEBS1, -2 and -3 [6]. The polyketide product is synthesized by the processive action of a loading didomain, six extension modules and a terminal thioesterase domain [5]. Each extension module contains a minimum of a ketosynthase (KS), an acyltransferase (AT) and an acyl-carrier protein (ACP). The KS domain both accepts the growing polyketide chain from the previous module and catalyses the subsequent decarboxylative condensation between this substrate and an ACP-bound methylmalonyl extender unit, introduce by the AT domain. This combined effort gives rise to a new polyketide intermediate that has been extended by two carbon atoms [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 87683-77-0
References:
1.  Omura, S. and Nakagawa, A. Biosynthesis of 16-membered macrolide antibiotics. Antibiotics 4 (1981) 175–192.
2.  Roberts, G. and Leadley, P.F. Use of [3H]tetrahydrocerulenin to assay condensing enzyme activity in Streptomyces erythreus. Biochem. Soc. Trans. 12 (1984) 642–643.
3.  Pfeifer, B.A., Admiraal, S.J., Gramajo, H., Cane, D.E. and Khosla, C. Biosynthesis of complex polyketides in a metabolically engineered strain of E. coli. Science 291 (2001) 1790–1792. [DOI] [PMID: 11230695]
4.  Tsai, S.C., Miercke, L.J., Krucinski, J., Gokhale, R., Chen, J.C., Foster, P.G., Cane, D.E., Khosla, C. and Stroud, R.M. Crystal structure of the macrocycle-forming thioesterase domain of the erythromycin polyketide synthase: versatility from a unique substrate channel. Proc. Natl. Acad. Sci. USA 98 (2001) 14808–14813. [DOI] [PMID: 11752428]
5.  Khosla, C., Tang, Y., Chen, A.Y., Schnarr, N.A. and Cane, D.E. Structure and mechanism of the 6-deoxyerythronolide B synthase. Annu. Rev. Biochem. 76 (2007) 195–221. [DOI] [PMID: 17328673]
[EC 2.3.1.94 created 1989, modified 2008]
 
 
EC 2.3.1.154      
Transferred entry: Propionyl-CoA C2-trimethyltridecanoyltransferase. Now EC 2.3.1.176, propanoyl-CoA C-acyltransferase.
[EC 2.3.1.154 created 2000, deleted 2015]
 
 
EC 2.3.1.168     
Accepted name: dihydrolipoyllysine-residue (2-methylpropanoyl)transferase
Reaction: 2-methylpropanoyl-CoA + enzyme N6-(dihydrolipoyl)lysine = CoA + enzyme N6-(S-[2-methylpropanoyl]dihydrolipoyl)lysine
For diagram of oxo-acid-dehydrogenase complexes, click here
Glossary: dihydrolipoyl group
Other name(s): dihydrolipoyl transacylase; enzyme-dihydrolipoyllysine:2-methylpropanoyl-CoA S-(2-methylpropanoyl)transferase; 2-methylpropanoyl-CoA:enzyme-6-N-(dihydrolipoyl)lysine S-(2-methylpropanoyl)transferase
Systematic name: 2-methylpropanoyl-CoA:enzyme-N6-(dihydrolipoyl)lysine S-(2-methylpropanoyl)transferase
Comments: A multimer (24-mer) of this enzyme forms the core of the multienzyme 3-methyl-2-oxobutanoate dehydrogenase complex, and binds tightly both EC 1.2.4.4, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) and EC 1.8.1.4, dihydrolipoyl dehydrogenase. The lipoyl group of this enzyme is reductively 2-methylpropanoylated by EC 1.2.4.4, and the only observed direction catalysed by EC 2.3.1.168 is that where this 2-methylpropanoyl is passed to coenzyme A. In addition to the 2-methylpropanoyl group, formed when EC 1.2.4.4 acts on the oxoacid that corresponds with valine, this enzyme also transfers the 3-methylbutanoyl and S-2-methylbutanoyl groups, donated to it when EC 1.2.4.4 acts on the oxo acids corresponding with leucine and isoleucine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 102784-26-9
References:
1.  Massey, L.K., Sokatch, J.R. and Conrad, R.S. Branched-chain amino acid catabolism in bacteria. Bacteriol. Rev. 40 (1976) 42–54. [PMID: 773366]
2.  Chuang, D.T., Hu, C.C., Ku, L.S., Niu, W.L., Myers, D.E. and Cox, R.P. Catalytic and structural properties of the dihydrolipoyl transacylase component of bovine branched-chain α-keto acid dehydrogenase. J. Biol. Chem. 259 (1984) 9277–9284. [PMID: 6746648]
3.  Wynn, R.M., Davie, J.R., Zhi, W., Cox, R.P. and Chuang, D.T. In vitro reconstitution of the 24-meric E2 inner core of bovine mitochondrial branched-chain α-keto acid dehydrogenase complex: requirement for chaperonins GroEL and GroES. Biochemistry 33 (1994) 8962–8968. [PMID: 7913832]
4.  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 2.3.1.168 created 2003]
 
 
EC 2.3.1.176     
Accepted name: propanoyl-CoA C-acyltransferase
Reaction: 3α,7α,12α-trihydroxy-5β-cholanoyl-CoA + propanoyl-CoA = CoA + 3α,7α,12α-trihydroxy-24-oxo-5β-cholestanoyl-CoA
For diagram of cholic acid biosynthesis (sidechain), click here
Other name(s): SCP2 (gene name); peroxisomal thiolase 2; sterol carrier protein-χ; SCPχ; PTE-2 (ambiguous); propionyl-CoA C2-trimethyltridecanoyltransferase; 3-oxopristanoyl-CoA hydrolase; 3-oxopristanoyl-CoA thiolase; peroxisome sterol carrier protein thiolase; sterol carrier protein; oxopristanoyl-CoA thiolase; peroxisomal 3-oxoacyl coenzyme A thiolase; SCPx; 4,8,12-trimethyltridecanoyl-CoA:propanoyl-CoA 2-C-4,8,12-trimethyltridecanoyltransferase
Systematic name: 3α,7α,12α-trihydroxy-5β-cholanoyl-CoA:propanoyl-CoA C-acyltransferase
Comments: Also acts on dihydroxy-5β-cholestanoyl-CoA and other branched chain acyl-CoA derivatives. The enzyme catalyses the penultimate step in the formation of bile acids. The bile acid moiety is transferred from the acyl-CoA thioester (RCO-SCoA) to either glycine or taurine (NH2R′) by EC 2.3.1.65, bile acid-CoA:amino acid N-acyltransferase [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Pedersen, J.I. and Gustafsson, J. Conversion of 3α,7α,12α-trihydroxy-5β-cholestanoic acid into cholic acid by rat liver peroxisomes. FEBS Lett. 121 (1980) 345–348. [DOI] [PMID: 7461136]
2.  Kase, F., Björkhem, I. and Pedersen, J.I. Formation of cholic acid from 3α,7α,12α-trihydroxy-5β-cholestanoic acid by rat liver peroxisomes. J. Lipid Res. 24 (1983) 1560–1567. [PMID: 6668450]
3.  Falany, C.N., Johnson, M.R., Barnes, S. and Diasio, R.B. Glycine and taurine conjugation of bile acids by a single enzyme. Molecular cloning and expression of human liver bile acid CoA:amino acid N-acyltransferase. J. Biol. Chem. 269 (1994) 19375–19379. [PMID: 8034703]
4.  Seedorf, U., Brysch, P., Engel, T., Schrage, K. and Assmann, G. Sterol carrier protein X is peroxisomal 3-oxoacyl coenzyme A thiolase with intrinsic sterol carrier and lipid transfer activity. J. Biol. Chem. 269 (1994) 21277–21283. [PMID: 8063752]
5.  Wanders, R.J.A., Denis, S., Wouters, F., Wirtz, K.W.A. and Seedorf, U. Sterol carrier protein X (SCPx) is a peroxisomal branched-chain β-ketothiolase specifically reacting with 3-oxo-pristanoyl-CoA: a new, unique role for SCPx in branched-chain fatty acid metabolism in peroxisomes. Biochem. Biophys. Res. Commun. 236 (1997) 565–569. [DOI] [PMID: 9245689]
6.  Russell, D.W. The enzymes, regulation, and genetics of bile acid synthesis. Annu. Rev. Biochem. 72 (2003) 137–174. [DOI] [PMID: 12543708]
[EC 2.3.1.176 created 2005 (EC 2.3.1.154 created 2000, incorporated 2015)]
 
 
EC 2.3.1.178     
Accepted name: diaminobutyrate acetyltransferase
Reaction: acetyl-CoA + L-2,4-diaminobutanoate = CoA + (2S)-4-acetamido-2-aminobutanoate
For diagram of ectoine biosynthesis, click here
Other name(s): L-2,4-diaminobutyrate acetyltransferase; L-2,4-diaminobutanoate acetyltransferase; EctA; diaminobutyric acid acetyltransferase; DABA acetyltransferase; 2,4-diaminobutanoate acetyltransferase; DAB acetyltransferase; DABAcT; acetyl-CoA:L-2,4-diaminobutanoate 4-N-acetyltransferase
Systematic name: acetyl-CoA:L-2,4-diaminobutanoate N4-acetyltransferase
Comments: Requires Na+ or K+ for maximal activity [3]. Ornithine, lysine, aspartate, and α-, β- and γ-aminobutanoate cannot act as substrates [3]. However, acetyl-CoA can be replaced by propanoyl-CoA, although the reaction proceeds more slowly [3]. Forms part of the ectoine-biosynthesis pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 130456-92-7
References:
1.  Peters, P., Galinski, E.A. and Truper, H.G. The biosynthesis of ectoine. FEMS Microbiol. Lett. 71 (1990) 157–162.
2.  Ono, H., Sawada, K., Khunajakr, N., Tao, T., Yamamoto, M., Hiramoto, M., Shinmyo, A., Takano, M. and Murooka, Y. Characterization of biosynthetic enzymes for ectoine as a compatible solute in a moderately halophilic eubacterium, Halomonas elongata. J. Bacteriol. 181 (1999) 91–99. [PMID: 9864317]
3.  Reshetnikov, A.S., Mustakhimov, I.I., Khmelenina, V.N. and Trotsenko, Y.A. Cloning, purification, and characterization of diaminobutyrate acetyltransferase from the halotolerant methanotroph Methylomicrobium alcaliphilum 20Z. Biochemistry (Mosc.) 70 (2005) 878–883. [PMID: 16212543]
4.  Kuhlmann, A.U. and Bremer, E. Osmotically regulated synthesis of the compatible solute ectoine in Bacillus pasteurii and related Bacillus spp. Appl. Environ. Microbiol. 68 (2002) 772–783. [DOI] [PMID: 11823218]
5.  Louis, P. and Galinski, E.A. Characterization of genes for the biosynthesis of the compatible solute ectoine from Marinococcus halophilus and osmoregulated expression in Escherichia coli. Microbiology 143 (1997) 1141–1149. [DOI] [PMID: 9141677]
[EC 2.3.1.178 created 2006]
 
 
EC 2.3.1.218     
Accepted name: phenylpropanoylacetyl-CoA synthase
Reaction: (1) feruloyl-CoA + malonyl-CoA = feruloylacetyl-CoA + CO2 + CoA
(2) 4-coumaroyl-CoA + malonyl-CoA = (4-coumaroyl)acetyl-CoA + CO2 + CoA
For diagram of curcumin biosynthesis, click here
Glossary: feruloylacetyl-CoA = feruloyl-diketide-CoA
(4-coumaroyl)acetyl-CoA = 4-coumaroyl-diketide-CoA
phenylpropanoylacetyl-CoA = phenylpropanoyl-diketide-CoA
Other name(s): phenylpropanoyl-diketide-CoA synthase; DCS
Systematic name: phenylpropanoyl-CoA:malonyl-CoA phenylpropanoyl-transferase (decarboxylating)
Comments: The enzyme has been characterized from the plant Curcuma longa (turmeric). It prefers feruloyl-CoA, and has no activity with cinnamoyl-CoA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Katsuyama, Y., Kita, T., Funa, N. and Horinouchi, S. Curcuminoid biosynthesis by two type III polyketide synthases in the herb Curcuma longa. J. Biol. Chem. 284 (2009) 11160–11170. [DOI] [PMID: 19258320]
[EC 2.3.1.218 created 2013]
 
 
EC 2.3.1.222     
Accepted name: phosphate propanoyltransferase
Reaction: propanoyl-CoA + phosphate = CoA + propanoyl phosphate
Other name(s): PduL
Systematic name: propanoyl-CoA:phosphate propanoyltransferase
Comments: Part of the degradation pathway for propane-1,2-diol .
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Liu, Y., Leal, N.A., Sampson, E.M., Johnson, C.L., Havemann, G.D. and Bobik, T.A. PduL is an evolutionarily distinct phosphotransacylase involved in B12-dependent 1,2-propanediol degradation by Salmonella enterica serovar typhimurium LT2. J. Bacteriol. 189 (2007) 1589–1596. [DOI] [PMID: 17158662]
[EC 2.3.1.222 created 2013]
 
 
EC 2.3.1.300     
Accepted name: branched-chain β-ketoacyl-[acyl-carrier-protein] synthase
Reaction: (1) 3-methylbutanoyl-CoA + a malonyl-[acyl-carrier protein] = a 5-methyl-3-oxohexanoyl-[acyl-carrier-protein] + CoA + CO2
(2) 2-methylpropanoyl-CoA + a malonyl-[acyl-carrier protein] = a 4-methyl-3-oxopentanoyl-[acyl-carrier-protein] + CoA + CO2
(3) (2S)-2-methylbutanoyl-CoA + a malonyl-[acyl-carrier protein] = a (4S)-4-methyl-3-oxohexanoyl-[acyl-carrier-protein] + CoA + CO2
Glossary: 3-methylbutanoyl-CoA = isovaleryl-CoA
2-methylpropanoyl-CoA = isobutanoyl-CoA = isobutyryl-CoA
Systematic name: 3-methylbutanoyl-CoA:malonyl-[acyl-carrier protein] C-acyltransferase
Comments: The enzyme is responsible for initiating branched-chain fatty acid biosynthesis by the dissociated (or type II) fatty-acid biosynthesis system (FAS-II) in some bacteria, using molecules derived from degradation of the branched-chain amino acids L-leucine, L-valine, and L-isoleucine to form the starting molecules for elongation by the FAS-II system. In some organisms the enzyme is also able to use acetyl-CoA, leading to production of a mix of branched-chain and straight-chain fatty acids [3] (cf. EC 2.3.1.180, β-ketoacyl-[acyl-carrier-protein] synthase III).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Han, L., Lobo, S. and Reynolds, K.A. Characterization of β-ketoacyl-acyl carrier protein synthase III from Streptomyces glaucescens and its role in initiation of fatty acid biosynthesis. J. Bacteriol. 180 (1998) 4481–4486. [DOI] [PMID: 9721286]
2.  Choi, K.H., Heath, R.J. and Rock, C.O. β-ketoacyl-acyl carrier protein synthase III (FabH) is a determining factor in branched-chain fatty acid biosynthesis. J. Bacteriol. 182 (2000) 365–370. [DOI] [PMID: 10629181]
3.  Khandekar, S.S., Gentry, D.R., Van Aller, G.S., Warren, P., Xiang, H., Silverman, C., Doyle, M.L., Chambers, P.A., Konstantinidis, A.K., Brandt, M., Daines, R.A. and Lonsdale, J.T. Identification, substrate specificity, and inhibition of the Streptococcus pneumoniae β-ketoacyl-acyl carrier protein synthase III (FabH). J. Biol. Chem. 276 (2001) 30024–30030. [DOI] [PMID: 11375394]
4.  Singh, A.K., Zhang, Y.M., Zhu, K., Subramanian, C., Li, Z., Jayaswal, R.K., Gatto, C., Rock, C.O. and Wilkinson, B.J. FabH selectivity for anteiso branched-chain fatty acid precursors in low-temperature adaptation in Listeria monocytogenes. FEMS Microbiol. Lett. 301 (2009) 188–192. [DOI] [PMID: 19863661]
5.  Yu, Y.H., Hu, Z., Dong, H.J., Ma, J.C. and Wang, H.H. Xanthomonas campestris FabH is required for branched-chain fatty acid and DSF-family quorum sensing signal biosynthesis. Sci. Rep. 6:32811 (2016). [DOI] [PMID: 27595587]
[EC 2.3.1.300 created 2021]
 
 
EC 2.3.3.5     
Accepted name: 2-methylcitrate synthase
Reaction: propanoyl-CoA + H2O + oxaloacetate = (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate + CoA
For diagram of reaction, click here
Glossary: 2-methylcitrate = (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate
Other name(s): 2-methylcitrate oxaloacetate-lyase; MCS; methylcitrate synthase; methylcitrate synthetase
Systematic name: propanoyl-CoA:oxaloacetate C-propanoyltransferase (thioester-hydrolysing, 1-carboxyethyl-forming)
Comments: The enzyme acts on acetyl-CoA, propanoyl-CoA, butanoyl-CoA and pentanoyl-CoA. The relative rate of condensation of acetyl-CoA and oxaloacetate is 140% of that of propanoyl-CoA and oxaloacetate, but the enzyme is distinct from EC 2.3.3.1, citrate (Si)-synthase. Oxaloacetate cannot be replaced by glyoxylate, pyruvate or 2-oxoglutarate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 57827-78-8
References:
1.  Uchiyama, H. and Tabuchi, T. Properties of methylcitrate synthase from Candida lipolytica. Agric. Biol. Chem. 40 (1976) 1411–1418.
2.  Textor, S., Wendisch, V.F., De Graaf, A.A., Muller, U., Linder, M.I., Linder, D. and Buckel, W. Propionate oxidation in Escherichia coli: evidence for operation of a methylcitrate cycle in bacteria. Arch. Microbiol. 168 (1997) 428–436. [PMID: 9325432]
3.  Horswill, A.R. and Escalante-Semerena, J.C. Salmonella typhimurium LT2 catabolizes propionate via the 2-methylcitric acid cycle. J. Bacteriol. 181 (1999) 5615–5623. [PMID: 10482501]
4.  Brock, M., Maerker, C., Schütz, A., Völker, U. and Buckel, W. Oxidation of propionate to pyruvate in Escherichia coli. Involvement of methylcitrate dehydratase and aconitase. Eur. J. Biochem. 269 (2002) 6184–6194. [DOI] [PMID: 12473114]
5.  Domin, N., Wilson, D. and Brock, M. Methylcitrate cycle activation during adaptation of Fusarium solani and Fusarium verticillioides to propionyl-CoA-generating carbon sources. Microbiology 155 (2009) 3903–3912. [DOI] [PMID: 19661181]
[EC 2.3.3.5 created 1978 as EC 4.1.3.31, transferred 2002 to EC 2.3.3.5, modified 2015]
 
 
EC 2.3.3.11     
Accepted name: 2-hydroxyglutarate synthase
Reaction: propanoyl-CoA + H2O + glyoxylate = 2-hydroxyglutarate + CoA
Other name(s): 2-hydroxyglutaratic synthetase; 2-hydroxyglutaric synthetase; α-hydroxyglutarate synthase; hydroxyglutarate synthase; 2-hydroxyglutarate glyoxylate-lyase (CoA-propanoylating)
Systematic name: propanoyl-CoA:glyoxylate C-propanoyltransferase (thioester-hydrolysing, 2-carboxyethyl-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9024-02-6
References:
1.  Reeves, H.C. and Ajl, S.J. α-Hydroxyglutaric acid synthetase. J. Bacteriol. 84 (1962) 186–187. [PMID: 14491016]
[EC 2.3.3.11 created 1965 as EC 4.1.3.9, transferred 2002 to EC 2.3.3.11]
 
 
EC 2.6.1.111     
Accepted name: 3-aminobutanoyl-CoA transaminase
Reaction: 3-aminobutanoyl-CoA + 2-oxoglutarate = acetoacetyl-CoA + L-glutamate
Other name(s): kat (gene name); acyl-CoA β-transaminase
Systematic name: 3-aminobutanoyl-CoA:2-oxoglutarate aminotransferase
Comments: The enzyme, found in bacteria, is part of a L-lysine degradation pathway. The enzyme is also active with other β-amino compounds such as 3-amino-5-methylhexanoyl-CoA and 3-amino-3-phenylpropanoyl-CoA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Perret, A., Lechaplais, C., Tricot, S., Perchat, N., Vergne, C., Pelle, C., Bastard, K., Kreimeyer, A., Vallenet, D., Zaparucha, A., Weissenbach, J. and Salanoubat, M. A novel acyl-CoA β-transaminase characterized from a metagenome. PLoS One 6:e22918 (2011). [DOI] [PMID: 21826218]
[EC 2.6.1.111 created 2017]
 
 
EC 2.8.3.1     
Accepted name: propionate CoA-transferase
Reaction: acetyl-CoA + propanoate = acetate + propanoyl-CoA
Other name(s): propionate coenzyme A-transferase; propionate-CoA:lactoyl-CoA transferase; propionyl CoA:acetate CoA transferase; propionyl-CoA transferase
Systematic name: acetyl-CoA:propanoate CoA-transferase
Comments: Butanoate and lactate can also act as acceptors.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD, CAS registry number: 9026-15-7
References:
1.  Stadtman, E.R. Acyl-coenzyme A synthesis by phosphotransacetylase and coenzyme A transphorase. Fed. Proc. 11 (1952) 291.
[EC 2.8.3.1 created 1961]
 
 
EC 2.8.3.14     
Accepted name: 5-hydroxypentanoate CoA-transferase
Reaction: acetyl-CoA + 5-hydroxypentanoate = acetate + 5-hydroxypentanoyl-CoA
Other name(s): 5-hydroxyvalerate CoA-transferase; 5-hydroxyvalerate coenzyme A transferase
Systematic name: acetyl-CoA:5-hydroxypentanoate CoA-transferase
Comments: Propanoyl-CoA, acetyl-CoA, butanoyl-CoA and some other acyl-CoAs can act as substrates, but more slowly than 5-hydroxypentanoyl-CoA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 111684-68-5
References:
1.  Eikmanns, U. and Buckel, W. Properties of 5-hydroxyvalerate CoA-transferase from Clostridium aminovalericum. Biol. Chem. Hoppe-Seyler 371 (1990) 1077–1082. [PMID: 2085413]
[EC 2.8.3.14 created 1992]
 
 
EC 2.8.3.20     
Accepted name: succinyl-CoA—D-citramalate CoA-transferase
Reaction: (1) succinyl-CoA + (R)-citramalate = succinate + (R)-citramalyl-CoA
(2) succinyl-CoA + (R)-malate = succinate + (R)-malyl-CoA
Glossary: (R)-citramalate = (2R)-2-hydroxy-2-methylbutanedioate
(R)-malate = (2R)-2-hydroxybutanedioate
(R)-malyl-CoA = (3R)-3-carboxy-3-hydroxypropanoyl-CoA
Other name(s): Sct
Systematic name: succinyl-CoA:(R)-citramalate CoA-transferase
Comments: The enzyme, purified from the bacterium Clostridium tetanomorphum, can also accept itaconate as acceptor, with lower efficiency.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Friedmann, S., Alber, B.E. and Fuchs, G. Properties of succinyl-coenzyme A:D-citramalate coenzyme A transferase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus. J. Bacteriol. 188 (2006) 6460–6468. [DOI] [PMID: 16952935]
[EC 2.8.3.20 created 2014]
 
 
EC 2.8.3.22     
Accepted name: succinyl-CoA—L-malate CoA-transferase
Reaction: (1) succinyl-CoA + (S)-malate = succinate + (S)-malyl-CoA
(2) succinyl-CoA + (S)-citramalate = succinate + (S)-citramalyl-CoA
For diagram of the 3-hydroxypropanoate cycle, click here
Glossary: (S)-citramalate = (2S)-2-hydroxy-2-methylbutanedioate
(S)-malate = (2S)-2-hydroxybutanedioate
(S)-malyl-CoA = (3S)-3-carboxy-3-hydroxypropanoyl-CoA
Other name(s): SmtAB
Systematic name: succinyl-CoA:(S)-malate CoA-transferase
Comments: The enzyme, purified from the bacterium Chloroflexus aurantiacus, can also accept itaconate as acceptor, with lower efficiency. It is part of the 3-hydroxypropanoate cycle for carbon assimilation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Friedmann, S., Steindorf, A., Alber, B.E. and Fuchs, G. Properties of succinyl-coenzyme A:L-malate coenzyme A transferase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus. J. Bacteriol. 188 (2006) 2646–2655. [DOI] [PMID: 16547052]
[EC 2.8.3.22 created 2014]
 
 
EC 2.8.3.23     
Accepted name: caffeate CoA-transferase
Reaction: 3-(3,4-dihydroxyphenyl)propanoyl-CoA + (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate = 3-(3,4-dihydroxyphenyl)propanoate + (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl-CoA
Glossary: 3-(3,4-dihydroxyphenyl)propanoate = hydrocaffeate
(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate = (2E)-3-(3,4-dihydroxyphenyl)acrylate = trans-caffeate
Other name(s): CarA
Systematic name: 3-(3,4-dihydroxyphenyl)propanoyl-CoA:(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate CoA-transferase
Comments: The enzyme, isolated from the bacterium Acetobacterium woodii, catalyses an energy-saving CoA loop for caffeate activation. In addition to caffeate, the enzyme can utilize 4-coumarate or ferulate as CoA acceptor.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hess, V., Gonzalez, J.M., Parthasarathy, A., Buckel, W. and Muller, V. Caffeate respiration in the acetogenic bacterium Acetobacterium woodii: a coenzyme A loop saves energy for caffeate activation. Appl. Environ. Microbiol. 79 (2013) 1942–1947. [DOI] [PMID: 23315745]
[EC 2.8.3.23 created 2015]
 
 
EC 3.1.2.4     
Accepted name: 3-hydroxyisobutyryl-CoA hydrolase
Reaction: 3-hydroxy-2-methylpropanoyl-CoA + H2O = CoA + 3-hydroxy-2-methylpropanoate
Other name(s): 3-hydroxy-isobutyryl CoA hydrolase; HIB CoA deacylase
Systematic name: 3-hydroxy-2-methylpropanoyl-CoA hydrolase
Comments: Also hydrolyses 3-hydroxypropanoyl-CoA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9025-88-1
References:
1.  Rendina, G. and Coon, M.J. Enzymatic hydrolysis of the coenzyme A thiol esters of β-hydroxypropionic and β-hydroxyisobutyric acids. J. Biol. Chem. 225 (1957) 523–534. [PMID: 13457352]
[EC 3.1.2.4 created 1961]
 
 
EC 3.1.2.18     
Accepted name: ADP-dependent short-chain-acyl-CoA hydrolase
Reaction: acyl-CoA + H2O = CoA + a carboxylate
Other name(s): short-chain acyl coenzyme A hydrolase; propionyl coenzyme A hydrolase; propionyl-CoA hydrolase; propionyl-CoA thioesterase; short-chain acyl-CoA hydrolase; short-chain acyl-CoA thioesterase
Systematic name: ADP-dependent-short-chain-acyl-CoA hydrolase
Comments: Requires ADP; inhibited by NADH. Maximum activity is shown with propanoyl-CoA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 117698-16-5
References:
1.  Alexson, S.E.H. and Nedergaard, J. A novel type of short- and medium-chain acyl-CoA hydrolases in brown adipose tissue mitochondria. J. Biol. Chem. 263 (1988) 13564–13571. [PMID: 2901416]
2.  Alexson, S.E.H., Svensson, L.T. and Nedergaard, J. NADH-sensitive propionyl-CoA hydrolase in brown-adipose-tissue mitochondria of the rat. Biochim. Biophys. Acta 1005 (1989) 13–19. [DOI] [PMID: 2570608]
[EC 3.1.2.18 created 1992]
 
 
EC 3.1.2.30     
Accepted name: (3S)-malyl-CoA thioesterase
Reaction: (S)-malyl-CoA + H2O = (S)-malate + CoA
Glossary: (S)-malate = (2S)-2-hydroxybutanedioate
(S)-malyl-CoA = (3S)-3-carboxy-3-hydroxypropanoyl-CoA
Other name(s): mcl2 (gene name)
Systematic name: (S)-malyl-CoA hydrolase
Comments: Stimulated by Mg2+ or Mn2+. The enzyme has no activity with (2R,3S)-2-methylmalyl-CoA (cf. EC 4.1.3.24, malyl-CoA lyase) or other CoA esters.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Erb, T.J., Frerichs-Revermann, L., Fuchs, G. and Alber, B.E. The apparent malate synthase activity of Rhodobacter sphaeroides is due to two paralogous enzymes, (3S)-malyl-coenzyme A (CoA)/β-methylmalyl-CoA lyase and (3S)-malyl-CoA thioesterase. J. Bacteriol. 192 (2010) 1249–1258. [DOI] [PMID: 20047909]
[EC 3.1.2.30 created 2014]
 
 
EC 3.13.1.4     
Accepted name: 3-sulfinopropanoyl-CoA desulfinase
Reaction: 3-sulfinopropanoyl-CoA + H2O = propanoyl-CoA + sulfite
Other name(s): 3SP-CoA desulfinase; AcdDPN7; 3-sulfinopropionyl-CoA desulfinase
Systematic name: 3-sulfinopropanoyl-CoA sulfinohydrolase
Comments: The enzyme from the β-proteobacterium Advenella mimigardefordensis contains one non-covalently bound FAD per subunit.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Schurmann, M., Deters, A., Wubbeler, J.H. and Steinbuchel, A. A novel 3-sulfinopropionyl coenzyme A (3SP-CoA) desulfinase from Advenella mimigardefordensis strain DPN7T acting as a key enzyme during catabolism of 3,3′-dithiodipropionic acid is a member of the acyl-CoA dehydrogenase superfamily. J. Bacteriol. 195 (2013) 1538–1551. [DOI] [PMID: 23354747]
2.  Schurmann, M., Demming, R.M., Krewing, M., Rose, J., Wubbeler, J.H. and Steinbuchel, A. Identification of 3-sulfinopropionyl coenzyme A (CoA) desulfinases within the Acyl-CoA dehydrogenase superfamily. J. Bacteriol. 196 (2014) 882–893. [DOI] [PMID: 24317404]
[EC 3.13.1.4 created 2014]
 
 
EC 4.1.1.41      
Transferred entry: (S)-methylmalonyl-CoA decarboxylase. Now EC 7.2.4.3, (S)-methylmalonyl-CoA decarboxylase
[EC 4.1.1.41 created 1972, modified 1983, modified 1986, deleted 2018]
 
 
EC 4.1.1.94     
Accepted name: ethylmalonyl-CoA decarboxylase
Reaction: (S)-ethylmalonyl-CoA = butanoyl-CoA + CO2
Systematic name: (S)-ethylmalonyl-CoA carboxy-lyase (butanoyl-CoA-forming)
Comments: The enzyme, which exists in all vertebrates, decarboxylates ethylmalonyl-CoA, a potentially toxic compound that is formed in low amounts by the activity of EC 6.4.1.2, acetyl-CoA carboxylase and EC 6.4.1.3, propanoyl-CoA carboxylase. It prefers the S isomer, and can decarboxylate (R)-ethylmalonyl-CoA with lower efficiency. cf. EC 7.2.4.1, (S)-methylmalonyl-CoA decarboxylase (sodium-transporting).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Linster, C.L., Noel, G., Stroobant, V., Vertommen, D., Vincent, M.F., Bommer, G.T., Veiga-da-Cunha, M. and Van Schaftingen, E. Ethylmalonyl-CoA decarboxylase, a new enzyme involved in metabolite proofreading. J. Biol. Chem. 286 (2011) 42992–43003. [DOI] [PMID: 22016388]
[EC 4.1.1.94 created 2012]
 
 
EC 4.1.2.41      
Transferred entry: vanillin synthase. Now included with EC 4.1.2.61, feruloyl-CoA hydratase/lyase
[EC 4.1.2.41 created 2000, deleted 2019]
 
 
EC 4.1.2.61     
Accepted name: feruloyl-CoA hydratase/lyase
Reaction: feruloyl-CoA + H2O = vanillin + acetyl-CoA (overall reaction)
(1a) feruloyl-CoA + H2O = 3-hydroxy-3-(4-hydroxy-3-methoxyphenyl)propanoyl-CoA
(1b) 3-hydroxy-3-(4-hydroxy-3-methoxyphenyl)propanoyl-CoA = vanillin + acetyl-CoA
Other name(s): hydroxycinnamoyl-CoA hydratase lyase; enoyl-CoA hydratase/aldolase; HCHL; ferB (gene name); couA (gene name)
Systematic name: feruloyl-CoA hydro-lyase/vanillin-lyase (acetyl-CoA-forming)
Comments: The enzyme is a member of the enoyl-CoA hydratase/isomerase superfamily. It catalyses a two-step process involving first the hydration of the double bond of feruloyl-CoA and then the cleavage of the resultant β-hydroxy thioester by retro-aldol reaction. (E)-caffeoyl-CoA and (E)-4-coumaroyl-CoA are also substrates.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Pometto, A.L. and Crawford, D.L. Whole-cell bioconversion of vanillin to vanillic acid by Streptomyces viridosporus. Appl. Environ. Microbiol. 45 (1983) 1582–1585. [PMID: 6870241]
2.  Narbad, A. and Gasson, M.J. Metabolism of ferulic acid via vanillin using a novel CoA-dependent pathway in a newly-isolated strain of Pseudomonas fluorescens. Microbiology 144 (1998) 1397–1405. [DOI] [PMID: 9611814]
3.  Gasson, M.J., Kitamura, Y., McLauchlan, W.R., Narbad, A., Parr, A.J., Parsons, E.L., Payne, J., Rhodes, M.J. and Walton, N.J. Metabolism of ferulic acid to vanillin. A bacterial gene of the enoyl-SCoA hydratase/isomerase superfamily encodes an enzyme for the hydration and cleavage of a hydroxycinnamic acid SCoA thioester. J. Biol. Chem. 273 (1998) 4163–4170. [PMID: 9461612]
4.  Overhage, J., Priefert, H. and Steinbuchel, A. Biochemical and genetic analyses of ferulic acid catabolism in Pseudomonas sp. Strain HR199. Appl. Environ. Microbiol. 65 (1999) 4837–4847. [PMID: 10543794]
5.  Bennett, J.P., Bertin, L., Moulton, B., Fairlamb, I.J., Brzozowski, A.M., Walton, N.J. and Grogan, G. A ternary complex of hydroxycinnamoyl-CoA hydratase-lyase (HCHL) with acetyl-CoA and vanillin gives insights into substrate specificity and mechanism. Biochem. J. 414 (2008) 281–289. [PMID: 18479250]
6.  Hirakawa, H., Schaefer, A.L., Greenberg, E.P. and Harwood, C.S. Anaerobic p-coumarate degradation by Rhodopseudomonas palustris and identification of CouR, a MarR repressor protein that binds p-coumaroyl coenzyme A. J. Bacteriol. 194 (2012) 1960–1967. [PMID: 22328668]
7.  Yang, W., Tang, H., Ni, J., Wu, Q., Hua, D., Tao, F. and Xu, P. Characterization of two Streptomyces enzymes that convert ferulic acid to vanillin. PLoS One 8:e67339 (2013). [PMID: 23840666]
[EC 4.1.2.61 created 2020 (EC 4.1.2.41 created 2000, incorporated 2020, EC 4.2.1.101 created 2000, incorporated 2020)]
 
 
EC 4.1.3.24     
Accepted name: malyl-CoA lyase
Reaction: (1) (S)-malyl-CoA = acetyl-CoA + glyoxylate
(2) (2R,3S)-2-methylmalyl-CoA = propanoyl-CoA + glyoxylate
For diagram of the 3-hydroxypropanoate cycle, click here
Glossary: (S)-malyl-CoA = (3S)-3-carboxy-3-hydroxypropanoyl-CoA
(2R,3S)-2-methylmalyl-CoA = L-erythro-β-methylmalyl-CoA = (2R,3S)-2-methyl-3-carboxy-3-hydroxypropanoyl-CoA
Other name(s): malyl-coenzyme A lyase; (3S)-3-carboxy-3-hydroxypropanoyl-CoA glyoxylate-lyase; mclA (gene name); mcl1 (gene name); (3S)-3-carboxy-3-hydroxypropanoyl-CoA glyoxylate-lyase (acetyl-CoA-forming); L-malyl-CoA lyase
Systematic name: (S)-malyl-CoA glyoxylate-lyase (acetyl-CoA-forming)
Comments: The enzymes from Rhodobacter species catalyse a step in the ethylmalonyl-CoA pathway for acetate assimilation [3,5]. The enzyme from halophilic bacteria participate in the methylaspartate cycle and catalyse the reaction in the direction of malyl-CoA formation [6]. The enzyme from the bacterium Chloroflexus aurantiacus, which participates in the 3-hydroxypropanoate cycle for carbon assimilation, also has the activity of EC 4.1.3.25, (3S)-citramalyl-CoA lyase [2,4].
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 37290-67-8
References:
1.  Tuboi, S. and Kikuchi, G. Enzymic cleavage of malyl-Coenzyme A into acetyl-Coenzyme A and glyoxylic acid. Biochim. Biophys. Acta 96 (1965) 148–153. [DOI] [PMID: 14285256]
2.  Herter, S., Busch, A. and Fuchs, G. L-Malyl-coenzyme A lyase/β-methylmalyl-coenzyme A lyase from Chloroflexus aurantiacus, a bifunctional enzyme involved in autotrophic CO2 fixation. J. Bacteriol. 184 (2002) 5999–6006. [DOI] [PMID: 12374834]
3.  Meister, M., Saum, S., Alber, B.E. and Fuchs, G. L-Malyl-coenzyme A/β-methylmalyl-coenzyme A lyase is involved in acetate assimilation of the isocitrate lyase-negative bacterium Rhodobacter capsulatus. J. Bacteriol. 187 (2005) 1415–1425. [DOI] [PMID: 15687206]
4.  Friedmann, S., Alber, B.E. and Fuchs, G. Properties of R-citramalyl-coenzyme A lyase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus. J. Bacteriol. 189 (2007) 2906–2914. [DOI] [PMID: 17259315]
5.  Erb, T.J., Frerichs-Revermann, L., Fuchs, G. and Alber, B.E. The apparent malate synthase activity of Rhodobacter sphaeroides is due to two paralogous enzymes, (3S)-malyl-coenzyme A (CoA)/β-methylmalyl-CoA lyase and (3S)-malyl-CoA thioesterase. J. Bacteriol. 192 (2010) 1249–1258. [DOI] [PMID: 20047909]
6.  Borjian, F., Han, J., Hou, J., Xiang, H., Zarzycki, J. and Berg, I.A. Malate Synthase and β-Methylmalyl Coenzyme A Lyase Reactions in the Methylaspartate Cycle in Haloarcula hispanica. J. Bacteriol. 199 (2017) . [DOI] [PMID: 27920298]
[EC 4.1.3.24 created 1972, modified 2014]
 
 
EC 4.2.1.101      
Transferred entry: trans-feruloyl-CoA hydratase. Now included with EC 4.1.2.61, feruloyl-CoA hydratase/lyase
[EC 4.2.1.101 created 2000, deleted 2020]
 
 
EC 4.2.1.116     
Accepted name: 3-hydroxypropionyl-CoA dehydratase
Reaction: 3-hydroxypropanoyl-CoA = acryloyl-CoA + H2O
For diagram of the 3-hydroxypropanoate cycle, click here and for diagram of the 3-hydroxypropanoate/4-hydroxybutanoate cycle and dicarboxylate/4-hydroxybutanoate cycle in archaea, click here
Glossary: acryloyl-CoA = acrylyl-CoA
3-hydroxypropanoyl-CoA = 3-hydroxypropionyl-CoA
Other name(s): 3-hydroxypropionyl-CoA hydro-lyase; 3-hydroxypropanoyl-CoA dehydratase
Systematic name: 3-hydroxypropanoyl-CoA hydro-lyase
Comments: Catalyses a step in the 3-hydroxypropanoate/4-hydroxybutanoate cycle, an autotrophic CO2 fixation pathway found in some thermoacidophilic archaea [1]. The enzyme from Metallosphaera sedula acts nearly equally as well on (S)-3-hydroxybutanoyl-CoA but not (R)-3-hydroxybutanoyl-CoA [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Berg, I.A., Kockelkorn, D., Buckel, W. and Fuchs, G. A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea. Science 318 (2007) 1782–1786. [DOI] [PMID: 18079405]
2.  Teufel, R., Kung, J.W., Kockelkorn, D., Alber, B.E. and Fuchs, G. 3-hydroxypropionyl-coenzyme A dehydratase and acryloyl-coenzyme A reductase, enzymes of the autotrophic 3-hydroxypropionate/4-hydroxybutyrate cycle in the Sulfolobales. J. Bacteriol. 191 (2009) 4572–4581. [DOI] [PMID: 19429610]
[EC 4.2.1.116 created 2009]
 
 
EC 4.2.1.148     
Accepted name: 2-methylfumaryl-CoA hydratase
Reaction: (2R,3S)-2-methylmalyl-CoA = 2-methylfumaryl-CoA + H2O
For diagram of the 3-hydroxypropanoate cycle, click here
Glossary: (2R,3S)-2-methylmalyl-CoA = L-erythro-β-methylmalyl-CoA = (2R,3S)-2-methyl-3-carboxy-3-hydroxypropanoyl-CoA
2-methylfumaryl-CoA = (E)-3-carboxy-2-methylprop-2-enoyl-CoA
Other name(s): Mcd; erythro-β-methylmalonyl-CoA hydrolyase; mesaconyl-coenzyme A hydratase (ambiguous); mesaconyl-C1-CoA hydratase
Systematic name: (2R,3S)-2-methylmalyl-CoA hydro-lyase (2-methylfumaryl-CoA-forming)
Comments: The enzyme from the bacterium Chloroflexus aurantiacus is part of the 3-hydroxypropanoate cycle for carbon assimilation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Zarzycki, J., Schlichting, A., Strychalsky, N., Muller, M., Alber, B.E. and Fuchs, G. Mesaconyl-coenzyme A hydratase, a new enzyme of two central carbon metabolic pathways in bacteria. J. Bacteriol. 190 (2008) 1366–1374. [DOI] [PMID: 18065535]
[EC 4.2.1.148 created 2014]
 
 
EC 4.2.1.155     
Accepted name: (methylthio)acryloyl-CoA hydratase
Reaction: 3-(methylsulfanyl)acryloyl-CoA + 2 H2O = acetaldehyde + methanethiol + CoA + CO2 (overall reaction)
(1a) 3-(methylsulfanyl)acryloyl-CoA + H2O = 3-hydroxy-3-(methylsulfanyl)propanoyl-CoA
(1b) 3-hydroxy-3-(methylsulfanyl)propanoyl-CoA = 3-oxopropanoyl-CoA + methanethiol
(1c) 3-oxopropanoyl-CoA + H2O = 3-oxopropanoate + CoA
(1d) 3-oxopropanoate = acetaldehyde + CO2
Glossary: 3-(methylsulfanyl)acryloyl-CoA = 3-(methylsulfanyl)prop-2-enoyl-CoA
Other name(s): DmdD
Systematic name: 3-(methylsulfanyl)prop-2-enoyl-CoA hydro-lyase (acetaldehyde-forming)
Comments: The enzyme is involved in the degradation of 3-(dimethylsulfonio)propanoate, an osmolyte produced by marine phytoplankton. Isolated from the bacterium Ruegeria pomeroyi.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Tan, D., Crabb, W.M., Whitman, W.B. and Tong, L. Crystal structure of DmdD, a crotonase superfamily enzyme that catalyzes the hydration and hydrolysis of methylthioacryloyl-CoA. PLoS One 8:e63870 (2013). [DOI] [PMID: 23704947]
[EC 4.2.1.155 created 2015]
 
 
EC 5.1.99.1     
Accepted name: methylmalonyl-CoA epimerase
Reaction: (R)-methylmalonyl-CoA = (S)-methylmalonyl-CoA
For diagram of the 3-hydroxypropanoate cycle, click here
Other name(s): methylmalonyl-CoA racemase; methylmalonyl coenzyme A racemase; DL-methylmalonyl-CoA racemase; 2-methyl-3-oxopropanoyl-CoA 2-epimerase [incorrect]
Systematic name: methylmalonyl-CoA 2-epimerase
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 9024-03-7
References:
1.  Mazumder, R., Sasakawa, T., Kaziro, Y. and Ochoa, S. Metabolism of propionic acid in animal tissues. IX. Methylmalonyl coenzyme A racemase. J. Biol. Chem. 237 (1962) 3065–3068. [PMID: 13934211]
2.  Overath, P., Kellerman, G.M., Lynen, F., Fritz, H.P. and Keller, H.J. Zum Mechanismus der Umlagerung von Methylmalonyl-CoA in Succinyl-CoA. II. Versuche zur Wirkungsweise von Methylmalonyl-CoA-Isomerase and Methylmalonyl-CoA-Racemase. Biochem. Z. 335 (1962) 500–518. [PMID: 14482843]
[EC 5.1.99.1 created 1965, modified 1981]
 
 
EC 5.4.99.2     
Accepted name: methylmalonyl-CoA mutase
Reaction: (R)-methylmalonyl-CoA = succinyl-CoA
For diagram of the 3-hydroxypropanoate cycle, click here
Other name(s): methylmalonyl-CoA CoA-carbonyl mutase; methylmalonyl coenzyme A mutase; methylmalonyl coenzyme A carbonylmutase; (S)-methylmalonyl-CoA mutase; (R)-2-methyl-3-oxopropanoyl-CoA CoA-carbonylmutase [incorrect]
Systematic name: (R)-methylmalonyl-CoA CoA-carbonylmutase
Comments: Requires a cobamide coenzyme.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, UM-BBD, CAS registry number: 9023-90-9
References:
1.  Barker, H.A. Coenzyme B12-dependent mutases causing carbon chain rearrangements. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 6, Academic Press, New York, 1972, pp. 509–537.
[EC 5.4.99.2 created 1961, modified 1983]
 
 
EC 5.4.99.13     
Accepted name: isobutyryl-CoA mutase
Reaction: 2-methylpropanoyl-CoA = butanoyl-CoA
Glossary: pivalate = 2,2-dimethylpropanoate
Other name(s): isobutyryl coenzyme A mutase; butyryl-CoA:isobutyryl-CoA mutase; icmA (gene name); icmB (gene name); icmF (gene name)
Systematic name: 2-methylpropanoyl-CoA CoA-carbonylmutase
Comments: This bacterial enzyme utilizes 5′-deoxyadenosylcobalamin as a cofactor. Following substrate binding, the enzyme catalyses the homolytic cleavage of the cobalt-carbon bond of AdoCbl, yielding cob(II)alamin and a 5′-deoxyadenosyl radical, which initiates the the carbon skeleton rearrangement reaction by hydrogen atom abstraction from the substrate. At the end of each catalytic cycle the 5′-deoxyadenosyl radical and cob(II)alamin recombine, regenerating the resting form of the cofactor. The enzyme is prone to inactivation resulting from occassional loss of the 5′-deoxyadenosyl molecule. Inactivated enzymes are repaired by the action of EC 2.5.1.17, cob(I)yrinic acid a,c-diamide adenosyltransferase, and a G-protein chaperone, which restore cob(II)alamin (which is first reduced to cob(I)alamin by an unidentified reductase) to 5′-deoxyadenosylcobalamin and load it back on the mutase. Some mutases are fused with their G-protein chaperone. These enzyme can also catalyse the interconversion of isovaleryl-CoA with pivalyl-CoA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 116405-23-3
References:
1.  Brendelberger, G., Rétey, J., Ashworth, D.M., Reynolds, K., Willenbrock, F. and Robinson, J.A. The enzymic interconversion of isobutyryl and N-butyrylcarba(dethia)-coenzyme-A - a coenzyme-B12-dependent carbon skeleton rearrangement. Angew. Chem. Int. Ed. Engl. 27 (1988) 1089–1091.
2.  Ratnatilleke, A., Vrijbloed, J.W. and Robinson, J.A. Cloning and sequencing of the coenzyme B12-binding domain of isobutyryl-CoA mutase from Streptomyces cinnamonensis, reconstitution of mutase activity, and characterization of the recombinant enzyme produced in Escherichia coli. J. Biol. Chem. 274 (1999) 31679–31685. [DOI] [PMID: 10531377]
3.  Cracan, V., Padovani, D. and Banerjee, R. IcmF is a fusion between the radical B12 enzyme isobutyryl-CoA mutase and its G-protein chaperone. J. Biol. Chem. 285 (2010) 655–666. [DOI] [PMID: 19864421]
4.  Cracan, V. and Banerjee, R. Novel coenzyme B12-dependent interconversion of isovaleryl-CoA and pivalyl-CoA. J. Biol. Chem. 287 (2012) 3723–3732. [DOI] [PMID: 22167181]
5.  Jost, M., Born, D.A., Cracan, V., Banerjee, R. and Drennan, C.L. Structural basis for substrate specificity in adenosylcobalamin-dependent isobutyryl-CoA mutase and related acyl-CoA mutases. J. Biol. Chem. 290 (2015) 26882–26898. [DOI] [PMID: 26318610]
6.  Li, Z., Kitanishi, K., Twahir, U.T., Cracan, V., Chapman, D., Warncke, K. and Banerjee, R. Cofactor editing by the G-protein metallochaperone domain regulates the radical B12 enzyme IcmF. J. Biol. Chem. 292 (2017) 3977–3987. [DOI] [PMID: 28130442]
[EC 5.4.99.13 created 1992, revised 2017]
 
 
EC 5.4.99.64     
Accepted name: 2-hydroxyisobutanoyl-CoA mutase
Reaction: 2-hydroxy-2-methylpropanoyl-CoA = (S)-3-hydroxybutanoyl-CoA
Glossary: 2-hydroxy-2-methylpropanoyl-CoA = 2-hydroxyisobutanoyl-CoA
Other name(s): hcmAB (gene names)
Systematic name: 2-hydroxy-2-methylpropanoyl-CoA mutase
Comments: The enzyme, characterized from the bacterium Aquincola tertiaricarbonis, uses radical chemistry to rearrange the positions of both a methyl group and a hydroxyl group. It consists of two subunits, the smaller one containing a cobalamin cofactor. It plays a central role in the degradation of assorted substrates containing a tert-butyl moiety.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Yaneva, N., Schuster, J., Schafer, F., Lede, V., Przybylski, D., Paproth, T., Harms, H., Muller, R.H. and Rohwerder, T. Bacterial acyl-CoA mutase specifically catalyzes coenzyme B12-dependent isomerization of 2-hydroxyisobutyryl-CoA and (S)-3-hydroxybutyryl-CoA. J. Biol. Chem. 287 (2012) 15502–15511. [DOI] [PMID: 22433853]
2.  Kurteva-Yaneva, N., Zahn, M., Weichler, M.T., Starke, R., Harms, H., Muller, R.H., Strater, N. and Rohwerder, T. Structural basis of the stereospecificity of bacterial B12-dependent 2-hydroxyisobutyryl-CoA mutase. J. Biol. Chem. 290 (2015) 9727–9737. [DOI] [PMID: 25720495]
[EC 5.4.99.64 created 2016 as EC 5.3.3.20, transferred 2017 to EC 5.4.99.64]
 
 
EC 6.2.1.17     
Accepted name: propionate—CoA ligase
Reaction: ATP + propanoate + CoA = AMP + diphosphate + propanoyl-CoA
Other name(s): propionyl-CoA synthetase
Systematic name: propanoate:CoA ligase (AMP-forming)
Comments: Propenoate can act instead of propanoate. Not identical with EC 6.2.1.1 (acetate—CoA ligase) or EC 6.2.1.2 (butyrate—CoA ligase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 55326-49-3
References:
1.  Ricks, C.A. and Cook, R.M. Regulation of volatile fatty acid uptake by mitochondrial acyl CoA synthetases of bovine liver. J. Dairy Sci. 64 (1981) 2324–2335. [DOI] [PMID: 7341659]
[EC 6.2.1.17 created 1984]
 
 
EC 6.2.1.36     
Accepted name: 3-hydroxypropionyl-CoA synthase
Reaction: 3-hydroxypropanoate + ATP + CoA = 3-hydroxypropanoyl-CoA + AMP + diphosphate
For diagram of the 3-hydroxypropanoate cycle, click here and for diagram of the 3-hydroxypropanoate/4-hydroxybutanoate cycle and dicarboxylate/4-hydroxybutanoate cycle in archaea, click here
Glossary: 3-hydroxypropionyl-CoA = 3-hydroxypropanoyl-CoA
Other name(s): 3-hydroxypropionyl-CoA synthetase (AMP-forming); 3-hydroxypropionate—CoA ligase
Systematic name: hydroxypropanoate:CoA ligase (AMP-forming)
Comments: Catalyses a step in the 3-hydroxypropanoate/4-hydroxybutanoate cycle, an autotrophic CO2 fixation pathway found in some thermoacidophilic archaea [1,2].The enzymes from Metallosphaera sedula and Sulfolobus tokodaii can also use propionate, acrylate, acetate, and butanoate as substrates [2], and are thus different from EC 6.2.1.17 (propionate—CoA ligase), which does not accept acetate or butanoate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Berg, I.A., Kockelkorn, D., Buckel, W. and Fuchs, G. A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea. Science 318 (2007) 1782–1786. [DOI] [PMID: 18079405]
2.  Alber, B.E., Kung, J.W. and Fuchs, G. 3-Hydroxypropionyl-coenzyme A synthetase from Metallosphaera sedula, an enzyme involved in autotrophic CO2 fixation. J. Bacteriol. 190 (2008) 1383–1389. [DOI] [PMID: 18165310]
[EC 6.2.1.36 created 2009]
 
 


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