3MPJ

Structure of the glutaryl-coenzyme A dehydrogenase

Summary for 3MPJ

• Entry DOI: 10.2210/pdb3mpj/pdb
• Related: 3MPI
• Descriptor: Glutaryl-CoA dehydrogenase, Octapeptide, FLAVIN-ADENINE DINUCLEOTIDE, ... (5 entities in total)
• Functional Keywords: alpha-beta fold, oxidoreductase
• Biological source: Desulfococcus multivorans; More
• Total number of polymer chains: 7
• Total formula weight: 266613.16

Authors

Wischgoll, S.,Warkentin, E.,Boll, M.,Ermler, U. (deposition date: 2010-04-27, release date: 2010-08-18, Last modification date: 2023-09-06)

Primary citation

Wischgoll, S.,Demmer, U.,Warkentin, E.,Gunther, R.,Boll, M.,Ermler, U.
Structural basis for promoting and preventing decarboxylation in glutaryl-coenzyme a dehydrogenases.
Biochemistry, 49:5350-5357, 2010

PubMed Abstract: Glutaryl-coenzyme A dehydrogenases (GDHs) involved in amino acid degradation were thought to catalyze both the dehydrogenation and decarboxylation of glutaryl-coenzyme A to crotonyl-coenzyme A and CO(2). Recently, a structurally related but nondecarboxylating, glutaconyl-coenzyme A-forming GDH was characterized in the obligately anaerobic bacteria Desulfococcus multivorans (GDH(Des)) which conserves the free energy of decarboxylation by a Na(+)-pumping glutaconyl-coenzyme A decarboxylase. To understand the distinct catalytic behavior of the two GDH types on an atomic basis, we determined the crystal structure of GDH(Des) with and without glutaconyl-coenzyme A bound at 2.05 and 2.1 A resolution, respectively. The decarboxylating and nondecarboxylating capabilities are provided by complex structural changes around the glutaconyl carboxylate group, the key factor being a Tyr --> Val exchange strictly conserved between the two GDH types. As a result, the interaction between the glutaconyl carboxylate and the guanidinium group of a conserved arginine is stronger in GDH(Des) (short and planar bidentate hydrogen bond) than in the decarboxylating human GDH (longer and monodentate hydrogen bond), which is corroborated by molecular dynamics studies. The identified structural changes prevent decarboxylation (i) by strengthening the C4-C5 bond of glutaconyl-coenzyme A, (ii) by reducing the leaving group potential of CO(2), and (iii) by increasing the distance between the C4 atom (negatively charged in the dienolate transition state) and the adjacent glutamic acid.

PubMed: 20486657
DOI: 10.1021/bi100317m

Experimental method

X-RAY DIFFRACTION (2.1 Å)