Dialkylglycine decarboxylase structure: alkali metal binding sites and bifunctional active site

Abstract

The structure of the pyridoxal phosphate dependent enzyme dialkylglycine decarboxylase (DGD) has been solved by X-ray crystallography. DGD catalyzes the oxidative decarboxylation of 2,2-dialkylglycines in the first half-reaction of its catalytic cycle, which is completed by a classical transamination half-reaction. The enzyme has two alkali metal ion binding sites, and two distinct structures differing in metal content were solved. One structure, DGD-K+, has a potassium ion bound at site 1, which is near the active site, and a sodium ion bound at site 2, which is at the surface of the molecule. The second structure, DGD-Na+, has sodium ions at both binding sites. The change in the active site structure due to the ion exchange at site 1 likely accounts for the dependence of DGD activity on K+ and the inhibitory effect of Na+. Models of the external aldimine intermediates with L-isovaline and L-alanine were built in order to provide insight into potential mechanisms of action. In both external aldimine models, the scissile bonds are held in an orientation perpendicular to the plane of the PLP ring plane, providing maximum stereoelectronic activation. In the L-isovaline model, the substrate carboxylate group makes hydrogen bonds with the side chain amide nitrogen of G1n52, the amino group of Lys272, and the guanidino group of Arg406. These interactions enable the enzyme to populate the productive conformation about Cα, in competition with a second, possibly more favorable but nonproductive one. This second conformation about Cα is found in our L-alanine model, where the substrate carboxylate group makes a double hydrogen bond-salt bridge interaction with Arg406. This conformation places the Cα-H bond perpendicular to the PLP ring plane, with the Lys272 amino group well positioned to provide general base catalysis of the transamination reaction.