Engineering substrate recognition sites of cytochrome P450 monooxygenase CYP116B3 from Rhodococcus ruber for enhanced regiospecific naphthalene hydroxylation

In this study, a cytochrome P450 monooxygenase CYP116B3 from Rhodococcus ruber was engineered to convert naphthalene selectively into 1-naphthol. The substrate recognition sites (SRSs) of CYP116B3 were identified using structure-based computational analysis. Subsequently, site-directed and saturation mutagenesis were conducted on SRS1, SRS2, and SRS3. The improved resulting triple mutant (E88C-N199Q-Q209A) was characterized. A final 1-naphthol titer of 8.26 mg/L/h was achieved, which is 14-fold higher than the control. The docking results suggest that the conformational changes produced by directed evolution improved the substrate binding environment. The results presented here hold promise for 1-naphthol production by P450 enzymes.