Crystal Structures of Active Fully Assembled Substrate- and Product-Bound Complexes of UDP- N -Acetylmuramic Acid: l -Alanine Ligase (MurC) from Haemophilus influenzae

Abstract

ABSTRACT UDP- N -acetylmuramic acid: l -alanine ligase (MurC) catalyzes the addition of the first amino acid to the cytoplasmic precursor of the bacterial cell wall peptidoglycan. The crystal structures of Haemophilus influenzae MurC in complex with its substrate UDP- N -acetylmuramic acid (UNAM) and Mg 2+ and of a fully assembled MurC complex with its product UDP- N -acetylmuramoyl- l -alanine (UMA), the nonhydrolyzable ATP analogue AMPPNP, and Mn 2+ have been determined to 1.85- and 1.7-Å resolution, respectively. These structures reveal a conserved, three-domain architecture with the binding sites for UNAM and ATP formed at the domain interfaces: the N-terminal domain binds the UDP portion of UNAM, and the central and C-terminal domains form the ATP-binding site, while the C-terminal domain also positions the alanine. An active enzyme structure is thus assembled at the common domain interfaces when all three substrates are bound. The MurC active site clearly shows that the γ-phosphate of AMPPNP is positioned between two bound metal ions, one of which also binds the reactive UNAM carboxylate, and that the alanine is oriented by interactions with the positively charged side chains of two MurC arginine residues and the negatively charged alanine carboxyl group. These results indicate that significant diversity exists in binding of the UDP moiety of the substrate by MurC and the subsequent ligases in the bacterial cell wall biosynthesis pathway and that alterations in the domain packing and tertiary structure allow the Mur ligases to bind sequentially larger UNAM peptide substrates.