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 |
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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] |
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[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] |
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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] |
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[EC 1.3.99.32 created 2012, modified 2013] |
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EC
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4.1.1.3
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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).
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[EC 4.1.1.3 created 1961 as EC 4.1.1.3, modified 1986, modified 2000, deleted 2018] |
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EC
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4.1.1.70
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Transferred entry: | glutaconyl-CoA decarboxylase. Now EC 7.2.4.5, glutaconyl-CoA decarboxylase
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[EC 4.1.1.70 created 1986, modified 2003, deleted 2019] |
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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] |
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[EC 4.1.3.26 created 1972] |
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EC |
4.2.1.18 |
Accepted name: |
methylglutaconyl-CoA hydratase |
Reaction: |
(S)-3-hydroxy-3-methylglutaryl-CoA = trans-3-methylglutaconyl-CoA + H2O |
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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] |
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[EC 4.2.1.18 created 1961] |
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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] |
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[EC 4.2.1.57 created 1972] |
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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] |
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[EC 4.2.1.167 created 2016] |
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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] |
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[EC 4.2.1.181 created 2023] |
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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. |
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[EC 6.4.1.4 created 1961] |
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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] |
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[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] |
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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] |
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[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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