Insight into the catalytic mechanism of meta-cleavage product hydrolase BphD: a quantum mechanics/molecular mechanics study

Abstract

The catalytic mechanism of BphD (meta-cleavage product hydrolase, the fourth enzyme of the biphenyl catabolic pathway) toward its natural substrate 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) was investigated in atomistic detail by the QM/MM approach. The calculated Boltzmann-weighted average barriers favor a substrate-assisted acylation mechanism, and the most feasible acylation pathway involves a catalytic triad (Ser-His-Asp). The product (2-hydroxypenta-2,4-dienoic acid) of the acylation process is replaced by three water molecules, and one of which is involved in the deacylation process. The established acylation and deacylation mechanism may shed light on investigating the degradation processes of wt BphD toward hundreds of other differently chlorinated HOPDA. The roles of seventeen residues during the catalytic process of wt BphD toward HOPDA were also reported in search of new promising experimental mutation targets for the improvement of BphD catalytic efficiency.