Catalytic mechanism of class A β-lactamase. I. The role of Glu166 and Ser130 in the deacylation reaction

Abstract

The tetrahedral intermediate formation process, which is the first step in the deacylation reaction by class A β-lactamase, was investigated by the ab initio molecular orbital method. In this study, benzyl penicillin was used as the substrate. From the results of our molecular dynamics study of the structure of β-lactam antibiotics-β-lactamase complex, the substrate, Ser70, Lys73, Ser130, Glu166 and a water molecule for the deacylation reaction were considered for construction of a model for calculation. The calculation results indicated that Glu166 plays a role in holding a water molecule, which is necessary for the deacylation reaction, and that the hydrogen bond network among Lys73Nζ, Ser130Oγ, and the carboxyl group of the β-lactam antibiotics was formed by the uptake of β-lactam antibiotics by β-lactamase. The activation energy for this reaction was 33.3 kcal/mol, and it is very likely that the reaction occurred at body temperature. Subsequent calculation results obtained by using the model excluding Ser130 and the carboxyl group of the substrate indicated that the activation energy for this reaction was 40.8 kcal/mol, which is 7.5 kcal/mol higher than that of the previous reaction. It was found that the hydrogen bond network plays an important role in decreasing the activation energy for the tetrahedral intermediate formation reaction. Lys73Nζ, which is located at the edge of the hydrogen bond network, played a role in forming a hydrogen bond with Glu166Oε in order to help the deacylation reaction. The role of amino acid residues around the active site of class A β-lactamase was also discussed.