Structural Basis for Promoting and Preventing Decarboxylation in Glutaryl-Coenzyme A Dehydrogenases

摘要

Glutaryl-coenzyme A dehydrogenases (GDHs) involved in amino acid degradation were thought toncatalyze both the dehydrogenation and decarboxylation of glutaryl-coenzyme A to crotonyl-coenzyme A andnCO2. Recently, a structurally related but nondecarboxylating, glutaconyl-coenzyme A-forming GDH wasncharacterized in the obligately anaerobic bacteria Desulfococcusmultivorans (GDHDes) which conserves the freenenergy of decarboxylation by a Naþ-pumping glutaconyl-coenzyme A decarboxylase. To understand the distinctncatalytic behavior of the two GDH types on an atomic basis, we determined the crystal structure of GDHDesnwith and without glutaconyl-coenzymeA bound at 2.05 and 2.1 Aresolution, respectively. The decarboxylatingnand nondecarboxylating capabilities are provided by complex structural changes around the glutaconylncarboxylate group, the key factor being a Tyr f Val exchange strictly conserved between the two GDH types.nAs a result, the interaction between the glutaconyl carboxylate and the guanidinium group of a conservednarginine is stronger inGDHDes (short and planar bidentate hydrogen bond) than in the decarboxylating humannGDH (longer and monodentate hydrogen bond), which is corroborated by molecular dynamics studies. Thenidentified structural changes prevent decarboxylation (i) by strengthening the C4-C5 bond of glutaconyl-ncoenzymeA, (ii) by reducing the leaving group potential of CO2, and (iii) by increasing the distance between thenC4 atom (negatively charged in the dienolate transition state) and the adjacent glutamic acid.