The Enzyme Database

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EC 1.3.8.6     
Accepted name: glutaryl-CoA dehydrogenase (ETF)
Reaction: glutaryl-CoA + electron-transfer flavoprotein = crotonyl-CoA + CO2 + reduced electron-transfer flavoprotein (overall reaction)
(1a) glutaryl-CoA + electron-transfer flavoprotein = (E)-glutaconyl-CoA + reduced electron-transfer flavoprotein
(1b) (E)-glutaconyl-CoA = crotonyl-CoA + CO2
For diagram of Benzoyl-CoA catabolism, click here
Glossary: (E)-glutaconyl-CoA = (2E)-4-carboxybut-2-enoyl-CoA
crotonyl-CoA = (E)-but-2-enoyl-CoA
Other name(s): glutaryl coenzyme A dehydrogenase; glutaryl-CoA:(acceptor) 2,3-oxidoreductase (decarboxylating); glutaryl-CoA dehydrogenase
Systematic name: glutaryl-CoA:electron-transfer flavoprotein 2,3-oxidoreductase (decarboxylating)
Comments: Contains FAD. The enzyme catalyses the oxidation of glutaryl-CoA to glutaconyl-CoA (which remains bound to the enzyme), and the decarboxylation of the latter to crotonyl-CoA (cf. EC 7.2.4.5, glutaconyl-CoA decarboxylase). FAD is the electron acceptor in the oxidation of the substrate, and its reoxidation by electron-transfer flavoprotein completes the catalytic cycle. The anaerobic, sulfate-reducing bacterium Desulfococcus multivorans contains two glutaryl-CoA dehydrogenases: a decarboxylating enzyme (this entry), and a non-decarboxylating enzyme that only catalyses the oxidation to glutaconyl-CoA [EC 1.3.99.32, glutaryl-CoA dehydrogenase (acceptor)].
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37255-38-2
References:
1.  Besrat, A., Polan, C.E. and Henderson, L.M. Mammalian metabolism of glutaric acid. J. Biol. Chem. 244 (1969) 1461–1467. [PMID: 4304226]
2.  Hartel, U., Eckel, E., Koch, J., Fuchs, G., Linder, D. and Buckel, W. Purification of glutaryl-CoA dehydrogenase from Pseudomonas sp., an enzyme involved in the anaerobic degradation of benzoate. Arch. Microbiol. 159 (1993) 174–181. [PMID: 8439237]
3.  Dwyer, T.M., Zhang, L., Muller, M., Marrugo, F. and Frerman, F. The functions of the flavin contact residues, αArg249 and βTyr16, in human electron transfer flavoprotein. Biochim. Biophys. Acta 1433 (1999) 139–152. [DOI] [PMID: 10446367]
4.  Rao, K.S., Albro, M., Dwyer, T.M. and Frerman, F.E. Kinetic mechanism of glutaryl-CoA dehydrogenase. Biochemistry 45 (2006) 15853–15861. [DOI] [PMID: 17176108]
[EC 1.3.8.6 created 1972 as EC 1.3.99.7, transferred 2012 to EC 1.3.8.6, modified 2013, modified 2019]
 
 
EC 1.3.99.32     
Accepted name: glutaryl-CoA dehydrogenase (acceptor)
Reaction: glutaryl-CoA + acceptor = (E)-glutaconyl-CoA + reduced acceptor
Glossary: (E)-glutaconyl-CoA = (2E)-4-carboxybut-2-enoyl-CoA
Other name(s): GDHDes; nondecarboxylating glutaryl-coenzyme A dehydrogenase; nondecarboxylating glutaconyl-coenzyme A-forming GDH; glutaryl-CoA dehydrogenase (non-decarboxylating)
Systematic name: glutaryl-CoA:acceptor 2,3-oxidoreductase (non-decarboxylating)
Comments: The enzyme contains FAD. The anaerobic, sulfate-reducing bacterium Desulfococcus multivorans contains two glutaryl-CoA dehydrogenases: a decarboxylating enzyme (EC 1.3.8.6), and a nondecarboxylating enzyme (this entry). The two enzymes cause different structural changes around the glutaconyl carboxylate group, primarily due to the presence of either a tyrosine or a valine residue, respectively, at the active site.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Wischgoll, S., Taubert, M., Peters, F., Jehmlich, N., von Bergen, M. and Boll, M. Decarboxylating and nondecarboxylating glutaryl-coenzyme A dehydrogenases in the aromatic metabolism of obligately anaerobic bacteria. J. Bacteriol. 191 (2009) 4401–4409. [DOI] [PMID: 19395484]
2.  Wischgoll, S., Demmer, U., Warkentin, E., Gunther, R., Boll, M. and Ermler, U. Structural basis for promoting and preventing decarboxylation in glutaryl-coenzyme A dehydrogenases. Biochemistry 49 (2010) 5350–5357. [DOI] [PMID: 20486657]
[EC 1.3.99.32 created 2012, modified 2013]
 
 
EC 4.1.1.3      
Transferred entry: oxaloacetate decarboxylase. Now recognized to be two enzymes EC 7.2.4.2 [oxaloacetate decarboxylase (Na+ extruding)] and EC 4.1.1.112 (oxaloacetate decarboxylase).
[EC 4.1.1.3 created 1961 as EC 4.1.1.3, modified 1986, modified 2000, deleted 2018]
 
 
EC 4.1.1.70      
Transferred entry: glutaconyl-CoA decarboxylase. Now EC 7.2.4.5, glutaconyl-CoA decarboxylase
[EC 4.1.1.70 created 1986, modified 2003, deleted 2019]
 
 
EC 4.1.3.26     
Accepted name: 3-hydroxy-3-isohexenylglutaryl-CoA lyase
Reaction: 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA = 7-methyl-3-oxooct-6-enoyl-CoA + acetate
Other name(s): β-hydroxy-β-isohexenylglutaryl CoA-lyase; hydroxyisohexenylglutaryl-CoA:acetatelyase; 3-hydroxy-3-isohexenylglutaryl coenzyme A lyase; 3-hydroxy-3-isohexenylglutaryl-CoA isopentenylacetoacetyl-CoA-lyase; 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA acetate-lyase
Systematic name: 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA acetate-lyase (7-methyl-3-oxooct-6-enoyl-CoA-forming)
Comments: Also acts on the hydroxy derivative of farnesoyl-CoA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37290-69-0
References:
1.  Seubert, W. and Fass, E. Untersuchungen über den bakterielle Abbau von Isoprenoiden. IV. Reinigung und Eigenschaftender β-Isohexenylglutaconyl-CoA-hydratase und β-Hydroxy-β-isohexenylglutaryl-CoA-lyase. Biochem. Z. 341 (1964) 23–34. [PMID: 14339651]
[EC 4.1.3.26 created 1972]
 
 
EC 4.2.1.18     
Accepted name: methylglutaconyl-CoA hydratase
Reaction: (S)-3-hydroxy-3-methylglutaryl-CoA = trans-3-methylglutaconyl-CoA + H2O
For diagram of mevalonate biosynthesis, click here
Other name(s): methylglutaconyl coenzyme A hydratase; 3-methylglutaconyl CoA hydratase; methylglutaconase; (S)-3-hydroxy-3-methylglutaryl-CoA hydro-lyase
Systematic name: (S)-3-hydroxy-3-methylglutaryl-CoA hydro-lyase (trans-3-methylglutaconyl-CoA-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9024-24-2
References:
1.  Hilz, H., Knappe, J., Ringelmann, E. and Lynen, F. Methylglutaconase, eine neue Hydratase, die am Stoffwechsel verzweigter Carbonsäuren beteiligt ist. Biochem. Z. 329 (1958) 476–489. [PMID: 13535602]
[EC 4.2.1.18 created 1961]
 
 
EC 4.2.1.57     
Accepted name: isohexenylglutaconyl-CoA hydratase
Reaction: 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA = 3-(4-methylpent-3-en-1-yl)pent-2-enedioyl-CoA + H2O
Other name(s): 3-hydroxy-3-isohexenylglutaryl-CoA-hydrolase; isohexenylglutaconyl coenzyme A hydratase; β-isohexenylglutaconyl-CoA-hydratase; 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA hydro-lyase
Systematic name: 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA hydro-lyase [3-(4-methylpent-3-en-1-yl)pent-2-enedioyl-CoA-forming]
Comments: Also acts on dimethylacryloyl-CoA and farnesoyl-CoA.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, CAS registry number: 37290-84-9
References:
1.  Seubert, W. and Fass, E. Untersuchungen über den bakterielle Abbau von Isoprenoiden. IV. Reinigung und Eigenschaftender β-Isohexenylglutaconyl-CoA-hydratase und β-Hydroxy-β-isohexenylglutaryl-CoA-lyase. Biochem. Z. 341 (1964) 23–34. [PMID: 14339651]
[EC 4.2.1.57 created 1972]
 
 
EC 4.2.1.167     
Accepted name: (R)-2-hydroxyglutaryl-CoA dehydratase
Reaction: (R)-2-hydroxyglutaryl-CoA = (E)-glutaconyl-CoA + H2O
Other name(s): hgdAB (gene names)
Systematic name: (R)-2-hydroxyglutaryl-CoA hydro-lyase ((E)-glutaconyl-CoA-forming)
Comments: The enzymes from the bacteria Acidaminococcus fermentans and Clostridium symbiosum are involved in the fermentation of L-glutamate. The enzyme contains [4Fe-4S] clusters, FMNH2 and riboflavin. It must be activated by an activator protein. Once activated, it can catalyse many turnovers.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Buckel, W. The reversible dehydration of (R)-2-hydroxyglutarate to (E)-glutaconate. Eur. J. Biochem. 106 (1980) 439–447. [DOI] [PMID: 7398622]
2.  Schweiger, G., Dutscho, R. and Buckel, W. Purification of 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. An iron-sulfur protein. Eur. J. Biochem. 169 (1987) 441–448. [DOI] [PMID: 3691501]
3.  Müller, U. and Buckel, W. Activation of (R)-2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. Eur. J. Biochem. 230 (1995) 698–704. [DOI] [PMID: 7607244]
4.  Hans, M., Sievers, J., Muller, U., Bill, E., Vorholt, J.A., Linder, D. and Buckel, W. 2-hydroxyglutaryl-CoA dehydratase from Clostridium symbiosum. Eur. J. Biochem. 265 (1999) 404–414. [DOI] [PMID: 10491198]
5.  Locher, K.P., Hans, M., Yeh, A.P., Schmid, B., Buckel, W. and Rees, D.C. Crystal structure of the Acidaminococcus fermentans 2-hydroxyglutaryl-CoA dehydratase component A. J. Mol. Biol. 307 (2001) 297–308. [DOI] [PMID: 11243821]
6.  Parthasarathy, A., Pierik, A.J., Kahnt, J., Zelder, O. and Buckel, W. Substrate specificity of 2-hydroxyglutaryl-CoA dehydratase from Clostridium symbiosum: toward a bio-based production of adipic acid. Biochemistry 50 (2011) 3540–3550. [DOI] [PMID: 21434666]
[EC 4.2.1.167 created 2016]
 
 
EC 4.2.1.181     
Accepted name: 3-carboxymethyl-3-hydroxy-acyl-[acp] dehydratase
Reaction: a 3-carboxymethyl-3-hydroxy-acyl-[acyl-carrier protein] = a 4-carboxy-3-alkylbut-2-enoyl-[acyl-carrier protein] + H2O
Other name(s): aprF (gene name); corF (gene name); curE (gene name); pedL (gene name); 3-carboxymethyl-3-hydroxy-acyl-[acyl-carrier protein] dehydratase
Systematic name: 3-carboxymethyl-3-hydroxy-acyl-[acyl-carrier protein] hydro-lyase
Comments: This family of enzymes participates in a process that introduces a methyl branch into nascent polyketide products. The process begins with EC 4.1.1.124, malonyl-[acp] decarboxylase, which converts the common extender unit malonyl-[acp] to acetyl-[acp]. The enzyme is a mutated form of a ketosynthase enzyme, in which a Cys residue in the active site is modified to a Ser residue, leaving the decarboxylase function intact, but nulifying the ability of the enzyme to form a carbon-carbon bond. Next, EC 2.3.3.22, 3-carboxymethyl-3-hydroxy-acyl-[acp] synthase, utilizes the acetyl group to introduce the branch at the β position of 3-oxoacyl intermediates attached to a polyketide synthase, forming a 3-hydroxy-3-carboxymethyl intermediate. This is followed by dehydration catalysed by EC 4.2.1.181, 3-carboxymethyl-3-hydroxy-acyl-[acp] dehydratase (often referred to as an ECH1 domain), leaving a 3-carboxymethyl group and forming a double bond between the α and β carbons. The process concludes with decarboxylation catalysed by EC 4.1.1.125, 4-carboxy-3-alkylbut-2-enoyl-[acp] decarboxylase (often referred to as an ECH2 domain), leaving a methyl branch at the β carbon. The enzymes are usually encoded by a cluster of genes referred to as an "HMGS cassette", based on the similarity of the key enzyme to EC 2.3.3.10, hydroxymethylglutaryl-CoA synthase. cf. EC 4.2.1.18, methylglutaconyl-CoA hydratase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Gu, L., Jia, J., Liu, H., Hakansson, K., Gerwick, W.H. and Sherman, D.H. Metabolic coupling of dehydration and decarboxylation in the curacin A pathway: functional identification of a mechanistically diverse enzyme pair. J. Am. Chem. Soc. 128 (2006) 9014–9015. [DOI] [PMID: 16834357]
2.  Gu, L., Wang, B., Kulkarni, A., Geders, T.W., Grindberg, R.V., Gerwick, L., Hakansson, K., Wipf, P., Smith, J.L., Gerwick, W.H. and Sherman, D.H. Metamorphic enzyme assembly in polyketide diversification. Nature 459 (2009) 731–735. [DOI] [PMID: 19494914]
3.  Erol, O., Schaberle, T.F., Schmitz, A., Rachid, S., Gurgui, C., El Omari, M., Lohr, F., Kehraus, S., Piel, J., Muller, R. and Konig, G.M. Biosynthesis of the myxobacterial antibiotic corallopyronin A. Chembiochem 11 (2010) 1253–1265. [DOI] [PMID: 20503218]
4.  Grindberg, R.V., Ishoey, T., Brinza, D., Esquenazi, E., Coates, R.C., Liu, W.T., Gerwick, L., Dorrestein, P.C., Pevzner, P., Lasken, R. and Gerwick, W.H. Single cell genome amplification accelerates identification of the apratoxin biosynthetic pathway from a complex microbial assemblage. PLoS One 6:e18565 (2011). [DOI] [PMID: 21533272]
[EC 4.2.1.181 created 2023]
 
 
EC 6.4.1.4     
Accepted name: methylcrotonoyl-CoA carboxylase
Reaction: ATP + 3-methylcrotonoyl-CoA + HCO3- = ADP + phosphate + 3-methylglutaconyl-CoA
Other name(s): methylcrotonyl coenzyme A carboxylase; β-methylcrotonyl coenzyme A carboxylase; β-methylcrotonyl CoA carboxylase; methylcrotonyl-CoA carboxylase
Systematic name: 3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)
Comments: A biotinyl-protein.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9023-95-4
References:
1.  Knappe, J., Schlegel, H.-G. and Lynen, F. Zur biochemischen Funktion des Biotins. I. Die Beteilligung der β-Methyl-crotonyl-Carboxylase an der Bildung von β-Hydroxy-β-methyl-glutaryl-CoA from β-Hydroxy-isovaleryl-CoA. Biochem. Z. 335 (1961) 101–122. [PMID: 14457200]
2.  Lynen, F., Knappe, J., Lorch, E., Jütting, G., Ringelmann, E. and Lachance, J.-P. Zur biochemischen Funktion des Biotins. II. Reinigung und Wirkungsweise der β-Methyl-crotonyl-Carboxlase. Biochem. Z. 335 (1961) 123–166. [PMID: 14467590]
3.  Rilling, H.C. and Coon, M.J. The enzymatic isomerization of α-methylvinylacetyl coenzyme A and the specificity of a bacterial α-methylcrotonyl coenzyme A carboxylase. J. Biol. Chem. 235 (1960) 3087–3092. [PMID: 13741692]
4.  Vagelos, P. Regulation of fatty acid biosynthesis. Curr. Top. Cell. Regul. 4 (1971) 119–166.
[EC 6.4.1.4 created 1961]
 
 
EC 7.2.4.2     
Accepted name: oxaloacetate decarboxylase (Na+ extruding)
Reaction: oxaloacetate + 2 Na+[side 1] = pyruvate + CO2 + 2 Na+[side 2]
Other name(s): oxaloacetate β-decarboxylase (ambiguous); oxalacetic acid decarboxylase (ambiguous); oxalate β-decarboxylase (ambiguous); oxaloacetate carboxy-lyase (ambiguous)
Systematic name: oxaloacetate carboxy-lyase (pyruvate-forming; Na+-extruding)
Comments: The enzyme from the bacterium Klebsiella aerogenes is a biotinyl protein and also decarboxylates glutaconyl-CoA and methylmalonyl-CoA. The process is accompanied by the extrusion of two sodium ions from cells. Some animal enzymes require Mn2+. Differs from EC 4.1.1.112 (oxaloacetate decarboxylase) for which there is no evidence for involvement in Na+ transport.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9024-98-0
References:
1.  Dimroth, P. Characterization of a membrane-bound biotin-containing enzyme: oxaloacetate decarboxylase from Klebsiella aerogenes. Eur. J. Biochem. 115 (1981) 353–358. [DOI] [PMID: 7016536]
2.  Dimroth, P. The role of biotin and sodium in the decarboxylation of oxaloacetate by the membrane-bound oxaloacetate decarboxylase from Klebsiella aerogenes. Eur. J. Biochem. 121 (1982) 435–441. [DOI] [PMID: 7037395]
[EC 7.2.4.2 created 1961 as EC 4.1.1.3, modified 1986, modified 2000, transferred 2018 to EC 7.2.4.2]
 
 
EC 7.2.4.5     
Accepted name: glutaconyl-CoA decarboxylase
Reaction: (2E)-4-carboxybut-2-enoyl-CoA + Na+[side 1] = (2E)-but-2-enoyl-CoA + CO2 + Na+[side 2]
Glossary: (E)-glutaconyl-CoA = (2E)-4-carboxybut-2-enoyl-CoA
Other name(s): glutaconyl coenzyme A decarboxylase; pent-2-enoyl-CoA carboxy-lyase; 4-carboxybut-2-enoyl-CoA carboxy-lyase
Systematic name: (2E)-4-carboxybut-2-enoyl-CoA carboxy-lyase [(2E)-but-2-enoyl-CoA-forming]
Comments: The enzyme from the bacterium Acidaminococcus fermentans is a biotinyl-protein, requires Na+, and acts as a sodium pump. Prior to the Na+-dependent decarboxylation, the carboxylate is transferred to biotin in a Na+-independent manner. The conserved lysine, to which biotin forms an amide bond, is located 34 amino acids before the C-terminus, flanked on both sides by two methionine residues, which are conserved in every biotin-dependent enzyme.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 84399-93-9
References:
1.  Buckel, W.S. and Semmler, R. Purification, characterisation and reconstitution of glutaconyl-CoA decarboxylase, a biotin-dependent sodium pump from anaerobic bacteria. Eur. J. Biochem. 136 (1983) 427–434. [DOI] [PMID: 6628393]
2.  Buckel, W. Sodium ion-translocating decarboxylases. Biochim. Biophys. Acta 1505 (2001) 15–27. [DOI] [PMID: 11248185]
[EC 7.2.4.5 created 1986 as EC 4.1.1.70, modified 2003, transferred 2019 to EC 7.2.4.5]
 
 


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