Degradation mechanism of biphenyl and 4-4′-dichlorobiphenyl cis-dihydroxylation by non-heme 2,3 dioxygenases BphA: A QM/MM approach

Biphenyl 2,3-dioxygenase (BphA), a Rieske-type and first enzyme in the aerobic degradation process, plays a key role in the metabolizing process of biphenyl/polychlorinated biphenyl aromatic pollutants in the environment. To understand the catalytic mechanism of biphenyl 2,3-dioxygenase, the conversions leading to the cis-diols are investigated by means of quantum mechanics/molecular mechanics (QM/MM) method. A hydroperoxo-iron (III) species is involved in the enzyme-catalyzed reaction. Herein, we explored the direct reaction mechanism of hydroperoxo-iron (III) species with biphenyl and 4-4'-dichlorobiphenyl. The reaction process involves an epoxide intermediate, it could develop into a carbocation intermediate, and ultimately evolve into a cis-diol product. The important roles of several residues during the dioxygenation process were highlighted. This study may provide theoretical support for further directed mutations and enzymatic engineering of BphA, as well as promote the development of degrading environmentally persistent biphenyl/polychlorinated biphenyl aromatic contaminants.