Structural and Mechanistic Analysis of Two Refined Crystal Structures of the Pyridoxal Phosphate-dependent Enzyme Dialkylglycine Decarboxylase

Abstract

Two refined structures, differing in alkali metal ion content, of the bifunctional, pyridoxal phosphate-dependent enzyme dialkylglycine decarboxylase (DGD) are presented in detail. The enzyme is an α tetramer, built up as a dimer of dimers, with a subunit molecular mass of 46.5 kDa. The fold of DGD is similar to those of aspartate aminotransferase, ω-amino acid aminotransferease and tyrosine phenol-lyase. The structure has two binding sites for alkali metal ions. GDG with potassium in site 1 (near the active site) and sodium in site 2 (at the surface of the molecule) has been refined against 2.6Å resolution data ( R-factor=17.6%), and DGD with sodium at both sites has been refined against 2.1 Å resolution data ( R-factor=17.8%). The proximity of site 1 to the active site accounts for the dependence of enzyme activity on potassium ions, and the observed active site structural changes caused by ion exchange at this site explain the inhibition of activity by sodium. DGD catalyzes both the decarboxylation of dialkylglycine species and the transamination of l-amino acids in its normal catalytic cycle. The active site structure of DGD is moderately homologous to that of aspartate aminotransferase, which catalyzes only transamination; both the differences and similarities provide mechanistic guidelines for the DGD-catalyzed reactions. Models of the l-isovaline and l-alanine external aldimine intermediates suggest mechanisms by which the decarboxylation and transamination reactions could be accomplished within the single active site. Decarboxylatio is proposed to be at least partially catalyzed by stereo-electronic activation of the C α-carboxylate bond achieved by orienting this bond perpendicular to the plane of the pyridinium ring in the dialkylglycine external aldimine intermediate. Transamination is proposed to be catalyzed by a similar effect on the C α-H bond of the l-amino acid external aldimine intermediate, combined with general base catalysis provided by Lys272, in analogy to the mechanism of as partate aminotransferase.