An Asymmetric Model for Na+-translocating Glutaconyl-CoA Decarboxylases

Abstract

Glutaconyl-CoA decarboxylase (Gcd) couples the biotin-dependent decarboxylation of glutaconyl-CoA with the generation of an electrochemical Na ؉ gradient. Sequencing of the genes encoding all subunits of the Clostridium symbiosum decarboxylase membrane complex revealed that it comprises two distinct biotin carrier subunits, GcdC 1 and GcdC 2 , which differ in the length of a central alanine-and proline-rich linker domain. Co-crystallization of the decarboxylase subunit GcdA with the substrate glutaconyl-CoA, the product crotonyl-CoA, and the substrate analogue glutaryl-CoA, respectively, resulted in a high resolution model for substrate binding and catalysis revealing remarkable structural changes upon substrate binding. Unlike the GcdA structure from Acidaminococcus fermentans, these data suggest that in intact Gcd complexes, GcdA is associated as a tetramer crisscrossed by a network of solventfilled tunnels.

Structure and function of biotin-dependent carboxylases

“…8E) is observed upon CoA binding in MCC [23]. A similar conformational change is also observed in GCDα [30]. …”

“…The connectivity between the N and C domains observed in MCC β subunit is the same as that in the α subunit of the Na + -transporting glutaconyl-CoA decarboxylase (GCDα) [27,30]. However, GCDα is a dimer only, and therefore the different connectivity leads to a distinct organization of the active site in GCDα dimer compared to the CT dimer of ACC (Fig.…”

“…The N1′ atom of biotin is ~6 Å from the γ carbon of the 3-methylcrotonyl-CoA substrate (Fig. 8E), modeled based on the observed positions of CoA bound to MCC [23] and crotonyl-CoA bound to GCDα [30]. A conformational change for two helices in the CT active site (α6 and α6A, Fig.…”

“…Biotin-dependent decarboxylases couple the decarboxylation of organic acids (possibly as CoA esters) to sodium ion transport in anaerobes [25–30], while the biotin-dependent transcarboxylase of Propionibacterium shermanii transfers the carboxyl group from methylmalonyl-CoA to pyruvate [31–33]. These enzymes are distinct from the biotin-dependent carboxylases in that they lack the BC component.…”

Fermentative Cyclohexane Carboxylate Formation in <b><i>Syntrophus aciditrophicus</i></b>

“…Hence, it is reasonable to propose that the glutaconyl-CoA decarboxylase from S. aciditrophicus works in both directions. Four genes, gcdABCD , encode the glutaconyl-CoA decarboxylases from several anaerobes [Kress et al, 2009]. In S. aciditrophicus only gcdABC ( SYN_00481, SYN_01431, SYN_00479 ) are present, whereas gcdD is missing.…”