Crystal structure of UDP-N-acetylmuramoyl-L-alanyl-D-glutamate: meso-diaminopimelate ligase from Escherichia coli

UDP-N-acetylmuramoyl-L-alanyl-D-glutamate aminopimelate ligase is a cytopla smic enzyme that catalyzes the addition of meso-diaminopimelic acid to nucl eotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate in the biosynthe sis of bacterial cell-wall peptidoglycan. The crystal structure of the Esch erichia coli enzyme in the presence of the final product of the enzymatic r eaction, UDP-MurNAc-L-Ala-gamma -D-Glu-meso-A(2)pm, has been solved to 2.0 Angstrom resolution. Phase information was obtained by multiwavelength anom alous dispersion using the K shell edge of selenium. The protein consists o f three domains, two of which have a topology reminiscent of the equivalent domain found in the already established three-dimensional structure of the UDP-N-acetylmuramoyl-L-alanine: D-glutamate-ligase (MurD) ligase, which ca talyzes the immediate previous step of incorporation of D-glutamic acid in the biosynthesis of the peptidoglycan precursor. The refined model reveals the binding site for UDP-MurNAc-L-Ala-gamma -D-Glu-meso-A(2)pm, and compari son with the six known MurD structures allowed the identification of residu es involved in the enzymatic mechanism. Interestingly, during refinement, a n excess of electron density was observed, leading to the conclusion that, as in MurD, a carbamylated lysine residue is present in the active site. In addition, the structural determinant responsible for the selection of the amino acid to be added to the nucleotide precursor was identified.