1SIR

The Crystal Structure and Mechanism of Human Glutaryl-CoA Dehydrogenase

Summary for 1SIR

• Entry DOI: 10.2210/pdb1sir/pdb
• Related: 1SIQ
• Descriptor: Glutaryl-CoA dehydrogenase, FLAVIN-ADENINE DINUCLEOTIDE, S-4-NITROBUTYRYL-COA, ... (4 entities in total)
• Functional Keywords: acyl-coa dehydrogenase, decoboxylation flavin protein, oxidoreductase
• Biological source: Homo sapiens (human)
• Cellular location: Mitochondrion matrix: Q92947
• Total number of polymer chains: 1
• Total formula weight: 45184.88

Authors

Wang, M.,Fu, Z.,Paschke, R.,Goodman, S.L.,Frerman, F.E.,Kim, J.J. (deposition date: 2004-03-01, release date: 2004-09-07, Last modification date: 2023-08-23)

Primary citation

Fu, Z.,Wang, M.,Paschke, R.,Rao, K.S.,Frerman, F.E.,Kim, J.J.
Crystal Structures of Human Glutaryl-CoA Dehydrogenase with and without an Alternate Substrate: Structural Bases of Dehydrogenation and Decarboxylation Reactions
Biochemistry, 43:9674-9684, 2004

PubMed Abstract: Acyl-CoA dehydrogenases (ACDs) are a family of flavoenzymes that metabolize fatty acids and some amino acids. Of nine known ACDs, glutaryl-CoA dehydrogenase (GCD) is unique: in addition to the alpha,beta-dehydrogenation reaction, common to all ACDs, GCD catalyzes decarboxylation of glutaryl-CoA to produce CO(2) and crotonyl-CoA. Crystal structures of GCD and its complex with 4-nitrobutyryl-CoA have been determined to 2.1 and 2.6 A, respectively. The overall polypeptide folds are the same and similar to the structures of other family members. The active site of the unliganded structure is filled with water molecules that are displaced when enzyme binds the substrate. The structure strongly suggests that the mechanism of dehydrogenation is the same as in other ACDs. The substrate binds at the re side of the FAD ring. Glu370 abstracts the C2 pro-R proton, which is acidified by the polarization of the thiolester carbonyl oxygen through hydrogen bonding to the 2'-OH of FAD and the amide nitrogen of Glu370. The C3 pro-R proton is transferred to the N(5) atom of FAD. The structures indicate a plausible mechanism for the decarboxylation reaction. The carbonyl polarization initiates decarboxylation, and Arg94 stabilizes the transient crotonyl-CoA anion. Protonation of the crotonyl-CoA anion occurs by a 1,3-prototropic shift catalyzed by the conjugated acid of the general base, Glu370. A tight hydrogen-bonding network involving gamma-carboxylate of the enzyme-bound glutaconyl-CoA, with Tyr369, Glu87, Arg94, Ser95, and Thr170, optimizes orientation of the gamma-carboxylate for decarboxylation. Some pathogenic mutations are explained by the structure. The mutations affect protein folding, stability, and/or substrate binding, resulting in inefficient/inactive enzyme.

PubMed: 15274622
DOI: 10.1021/bi049290c

Experimental method

X-RAY DIFFRACTION (2.6 Å)