A Computational Evaluation of the Mechanism of Penicillin-Binding Protein-Catalyzed Cross-Linking of the Bacterial Cell Wall

作者：Shi Qicun; Meroueh Samy O; Fisher Jed F; Mobashery Shahriar^*

来源：Journal of the American Chemical Society, 2011, 133(14): 5274-5283.

DOI：10.1021/ja1074739

Penicillin-binding protein 1b (PBP 1b) of the Gram-positive bacterium Streptococcus pneumoniae catalyzes the cross-linking of adjacent peptidoglycan strands, as a critical event in the biosynthesis of its cell wall. This enzyme is representative of the biosynthetic PBP structures of the beta-lactam-recognizing enzyme superfamily and is the target of the beta-lactam antibiotics. In the cross-linking reaction, the amide between the -D-Ala-D-Ala dipeptide at the terminus of a peptide stem acts as an acyl donor toward the epsilon-amino group of a lysine found on an adjacent stem. The mechanism of this transpeptidation was evaluated using explicit-solvent molecular dynamics simulations and ONIOM quantum mechanics/molecular mechanics calculations. Sequential acyl transfer occurs to, and then from, the active site serine. The resulting cross-link is predicted to have a cis-amide configuration. The ensuing and energetically favorable cis- to trans-amide isomerization, within the active site, may represent the key event driving product release to complete enzymatic turnover.

• 出版日期2011-4-13