Reaction Mechanism of Escherichia coli Dihydrodipicolinate Synthase Investigated by X-ray Crystallography and NMR Spectroscopy

Dihydrodipicolinate synthase (DHDPS) catalyzes the condensation of pyruvate with l-aspartate β-semialdehyde. It is the first enzyme unique to the diaminopimelate pathway of lysine biosynthesis. Here we present the crystal structures of five complexes of Escherichia coli DHDPS with substrates, substrate analogs, and inhibitors. These include the complexes of DHDPS with (1) pyruvate, (2) pyruvate and the l-aspartate β-semialdehyde analog succinate β-semialdehyde, (3) the inhibitor α-ketopimelic acid, (4) dipicolinic acid, and (5) the natural feedback inhibitor l-lysine. The kinetics of inhibition were determined, and the binding site of the l-lysine was identified. NMR experiments were conducted in order to elucidate the nature of the product of the reaction catalyzed by DHDPS. By this method, (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid is identified as the only product. A reaction mechanism for DHDPS is proposed, and important features for inhibition are identified.