Identification of Glu166 as the General Base in the Acylation Reaction of Class A β-Lactamases through QM/MM Modeling

Abstract

Bacterial class A β-lactamases are responsible for the most known resistance against β-lactam antibiotics. With the continuing rise in antibiotic resistance, improved knowledge of the mechanisms of action of these enzymes is needed in the development of effective therapeutic agents and strategies. The mechanism of the deacylation step in class A β-lactamases is well accepted. In contrast, the mechanism of the acylation step has been uncertain, with several conflicting proposals put forward. We have modeled the acylation step in a class A β-lactamase, using a combined quantum mechanics/molecular mechanics approach. The results provide an atomic level description of the reaction and show that Glu166 acts as the general base in the reaction, deprotonating Ser70 via an intervening water molecule. Ser70 acts as the nucleophile for attack on the lactam ring in a concerted reaction. The results do not rule out the importance of Lys73 in catalysis, in agreement with experimental data.