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, EXPASY, KEGG, MetaCyc, PDB, UM-BBD, 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
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 4.2.1.167     
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 [4F-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 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, EXPASY, KEGG, MetaCyc, PDB, UM-BBD, 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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