Crystal structures of dialkylglycine decarboxylase inhibitor complexes

The crystal structures of four inhibitor complexes of dialkylglycine decarb oxylase are reported. The enzyme does not undergo a domain closure, as does aspartate aminotransferase, upon inhibitor binding. Two active-site confor mations have been observed in previous structures that differ in alkali met al ion content, and two active-site conformations have been shown to coexis t in solution when a single type of metal ion is present. There is no indic ation of coexisting conformers in the structures reported here or in the pr eviously reported structures, and the observed conformation is that expecte d based on the presence of potassium in the enzyme. Thus, although two acti ve-site conformations coexist in solution, a single conformation, correspon ding to the more active enzyme, predominates in the crystal. The structure of 1-aminocyclopropane-1-carboxylate bound in the active site shows the ald imine double bond to the pyridoxal phosphate cofactor to be fully out of th e plane of the coenzyme ring, whereas the C alpha-CO2- bond lies close to i t. This provides an explanation for the observed lack of decarboxylation re activity with this amino acid. The carboxylate groups of both 1-aminocyclop ropane-1-carboxylate and 5'-phosphopyridoxyl-2-methylalanine interact with Ser215 and Arg406 as previously proposed. This demonstrates structurally th at alternative binding modes, which constitute substrate inhibition, occur in the decarboxylation half-reaction The structures of D and L-cycloserine bound to the active-site show that the L-isomer is deprotonated at C-alpha, presumably by Lys272, while the D-isomer is not. This difference explains the similar to 3000-fold greater potency of the L versus the D-isomer as a competitive inhibitor of dialkylglycine decarboxylase. (C) 1999 Academic Pr ess.