Modeling study on a hydrolytic mechanism of class A beta-lactamases

Comparison of the hydrogen-bond networks at the active site in the crystallographic structures reported for class A beta-lactamases revealed an importance of a switch of the hydrogen-bond network for the catalytic process. Taking account of the conformational mobility of the Lys73 residue, we have constructed putative complex models for beta-lactam antibiotics and the enzymes in the multistep hydrolysis which consists of a Michaelis complex, an acyl-enzyme, and a tetrahedral oxyanion for deacylation. In the acylation, the C3 carboxylate of penicillin derivatives would participate in activation of the Ser130 hydroxyl group and then the oxyanion of the Ser130 residue would deprotonate the ammonium group of the Lys73 residue which will act as a general base for activation of the Ser70 residue. In the deacylation, the deacylating water molecule would be accommodated during a conformational change of the acyl moiety without a structural change of the active-site residues and the unprotonated N4 atom of the penicillins would act as a general base to activate the water molecule. This catalytic process provided a new account for the stability of the acyl-enzyme complexes. This substrate-assisted mechanism would also be extended to a hydrolytic mechanism of class C enzymes.