title: A computational evaluation of the mechanism of penicillin-binding protein-catalyzed cross-linking of the bacterial cell wall.
abstract: 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 β-lactam-recognizing enzyme superfamily and is the target of the β-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 ε-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.
authors.affiliation: Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA.
authors.forename: Qicun
authors.initials: Q
authors.lastname: Shi
authors.forename: Samy O
authors.initials: SO
authors.lastname: Meroueh
authors.forename: Jed F
authors.initials: JF
authors.lastname: Fisher
authors.forename: Shahriar
authors.initials: S
authors.lastname: Mobashery
mesh_terms: D055162:Biocatalysis; D002473:Cell Wall / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D046915:Penicillin-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D011487:Protein Conformation; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry; D013296:Streptococcus pneumoniae / Q000166:cytology* / Q000201:enzymology* / Q000378:metabolism
chemical_list: D046915:Penicillin-Binding Proteins; D012997:Solvents