PDBsum entry 2r0m

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Oxidoreductase PDB id
Protein chain
390 a.a. *
Waters ×48
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: The effect of a glu370asp mutation in glutaryl-coa dehydrogenase on proton transfer to the dienolate intermediate
Structure: Glutaryl-coa dehydrogenase. Chain: a. Synonym: gcd. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
2.70Å     R-factor:   0.191     R-free:   0.240
Authors: K.S.Rao,Z.Fu,M.Albro,B.Narayanan,S.Baddam,H.J.Lee,J.J.Kim, F.E.Frerman
Key ref: K.S.Rao et al. (2007). The effect of a Glu370Asp mutation in glutaryl-CoA dehydrogenase on proton transfer to the dienolate intermediate. Biochemistry, 46, 14468-14477. PubMed id: 18020372 DOI: 10.1021/bi7009597
20-Aug-07     Release date:   22-Apr-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q92947  (GCDH_HUMAN) -  Glutaryl-CoA dehydrogenase, mitochondrial
438 a.a.
390 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Glutaryl-CoA dehydrogenase (ETF).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Glutaryl-CoA + electron-transfer flavoprotein = crotonyl-CoA + CO2 + reduced electron-transfer flavoprotein
+ electron-transfer flavoprotein
= crotonyl-CoA
+ CO(2)
+ reduced electron-transfer flavoprotein
      Cofactor: FAD
Bound ligand (Het Group name = FAD) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     mitochondrion   3 terms 
  Biological process     metabolic process   9 terms 
  Biochemical function     oxidoreductase activity     6 terms  


DOI no: 10.1021/bi7009597 Biochemistry 46:14468-14477 (2007)
PubMed id: 18020372  
The effect of a Glu370Asp mutation in glutaryl-CoA dehydrogenase on proton transfer to the dienolate intermediate.
K.S.Rao, Z.Fu, M.Albro, B.Narayanan, S.Baddam, H.J.Lee, J.J.Kim, F.E.Frerman.
We have determined steady-state rate constants and net rate constants for the chemical steps in the catalytic pathway catalyzed by the E370D mutant of glutaryl-CoA dehydrogenase and compared them with those of the wild-type dehydrogenase. We sought rationales for changes in these rate constants in the structure of the mutant cocrystallized with the alternate substrate, 4-nitrobutyric acid. Substitution of aspartate for E370, the catalytic base, results in a 24% decrease in the rate constant for proton abstraction at C-2 of 3-thiaglutaryl-CoA as the distance between C-2 of the ligand and the closest carboxyl oxygen at residue 370 increases from 2.9 A to 3.1 A. The net rate constant for flavin reduction due to hydride transfer from C-3 of the natural substrate, which includes proton abstraction at C-2, to N5 of the flavin decreases by 81% due to the mutation, although the distance increases only by 0.7 A. The intensities of charge-transfer bands associated with the enolate of 3-thiaglutaryl-CoA, the reductive half-reaction (reduced flavin with oxidized form of substrate), and the dienolate following decarboxylation are considerably diminished. Structural investigation suggests that the increased distance and the change in angle of the S-C1(=O)-C2 plane of the substrate with the isoalloxazine substantially alter rates of the reductive and oxidative half-reactions. This change in active site geometry also changes the position of protonation of the four carbon dienolate intermediate to produce kinetically favorable product, vinylacetyl-CoA, which is further isomerized to the thermodynamically stable normal product, crotonyl-CoA.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21477586 J.Schaarschmidt, S.Wischgoll, H.J.Hofmann, and M.Boll (2011).
Conversion of a decarboxylating to a non-decarboxylating glutaryl-coenzyme A dehydrogenase by site-directed mutagenesis.
  FEBS Lett, 585, 1317-1321.  
19395484 S.Wischgoll, M.Taubert, F.Peters, N.Jehmlich, M.von Bergen, and M.Boll (2009).
Decarboxylating and nondecarboxylating glutaryl-coenzyme A dehydrogenases in the aromatic metabolism of obligately anaerobic bacteria.
  J Bacteriol, 191, 4401-4409.  
18775954 B.Keyser, C.Mühlhausen, A.Dickmanns, E.Christensen, N.Muschol, K.Ullrich, and T.Braulke (2008).
Disease-causing missense mutations affect enzymatic activity, stability and oligomerization of glutaryl-CoA dehydrogenase (GCDH).
  Hum Mol Genet, 17, 3854-3863.  
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