Catalytic cycle of penicillin acylase from Escherichia coli: QM/MM modeling of chemical transformations in the enzyme active site upon penicillin G hydrolysis

Penicillin acylase from Escherichia coli is a unique enzyme that belongs to the recently discovered superfamily of N-terminal nucleophile hydrolases. It catalyzes selective hydrolysis of the side chain amide bond of penicillins and cephalosporins while leaving the labile amide bond in the β-lactam ring intact. Despite wide applications of penicillin acylase in the industry of β-lactam antibiotics and production of chiral amino compounds, its catalytic mechanism at atomic resolution has not yet been characterized. The complete cycle of chemical transformations of the most specific substrate of the enzyme, penicillin G, leading to formation of 6-aminopenicillanic and phenylacetic acids was modeled following quantum mechanics–molecular mechanics (QM/MM) calculations of the minimum energy reaction profile. The active site residues and the substrate were included in the QM part, and the rest of the system was treated applying molecular mechanics and classical force field parameters. The 3D structures in the en...