Insights into the Base Catalysis Exerted by the DD-Transpeptidase from Streptomyces K15:  A Molecular Dynamics Study^†

Herein, we present results from molecular dynamics simulations of the DD-transpeptidase/penicillin-binding protein from Streptomyces K15 and its Michaelis complex with benzylpenicillin. For the apo-enzyme, six different configurations of the active site were modeled in aqueous solution and their relative stabilities were estimated by means of quantum mechanical energy calculations. The energetically most stable configuration has a neutral Lys₂₁₃ residue. In this configuration, the nucleophilic Ser₃₅ hydroxyl group interchanges with a water molecule in the “oxy-anion hole” and the Lys₃₈/Lys₂₁₃ ammonium/amino groups are connected through the Ser₉₆ hydroxyl group. Subsequently, the enzyme−penicillin complexes corresponding to the four most stable configurations of the apo-enzyme were modeled. In the presence of the β-lactam antibiotic, the configuration with a neutral Lys₃₈ residue is favored energetically and shows the best orientation for nucleophilic attack. In addition, a very stable contact between the Ser₃₅ hydroxyl group and the neutral amino group of Lys₃₈ supports the assignation of Lys₃₈ as the base catalyst for the acylation step. Finally, some mechanistic implications of enzyme−inhibitor contacts involving the benzylpenicillin carboxylate group are also discussed.