The three-dimensional structure of the ternary complex of Corynebacterium glutamicum diaminopimelate dehydrogenase-NADPH-l-2-amino-6-methylene-pimelate

Abstract

The three-dimensional (3D) structure of Corynebacterium glutamicum diaminopimelate d-dehydrogenase in a ternary complex with NADPH and l-2-amino-6-methylene-pimelate has been solved and refined to a resolution of 2.1 Å. l-2-Amino-6-methylene-pimelate was recently synthesized and shown to be a potent competitive inhibitor (5 μM) vs. meso-diaminopimelate of the Bacillus sphaericus dehydrogenase (Sutherland et al., 1999). Diaminopimelate dehydrogenase catalyzes the reversible NADP⁺-dependent oxidation of the d-amino acid stereocenter of meso-diaminopimelate, and is the only enzyme known to catalyze the oxidative deamination of a d-amino acid. The enzyme is involved in the biosynthesis of meso-diaminopimelate and l-lysine from l-aspartate, a biosynthetic pathway of considerable interest because it is essential for growth of certain bacteria. The dehydrogenase is found in a limited number of species of bacteria, as opposed to the alternative succinylase and acetylase pathways that are widely distributed in bacteria and plants. The structure of the ternary complex reported here provides a structural rationale for the nature and potency of the inhibition exhibited by the unsaturated l-2-amino-6-methylene-pimelate against the dehydrogenase. In particular, we compare the present structure with other structures containing either bound substrate, meso-diaminopimelate, or a conformationally restricted isoxazoline inhibitor. We have identified a significant interaction between the α-l-amino group of the unsaturated inhibitor and the indole ring of Trp144 that may account for the tight binding of this inhibitor.