Tuning enzymatic properties by protein engineering toward catalytic tetrad of carbonyl reductase

Enzyme engineering toward catalytic-tetrad residues usually results in activity loss. Unexpectedly, we found that a directed evolution campaign yielded a beneficial residue A100 in KmCR (a carbonyl reductase from Kluyveromyces marxianus ZJB14056), which is a residue of catalytic tetrad and conserved according to multiple sequence alignment. Inspired by this finding, we performed saturation mutagenesis on all the four residues of catalytic tetrad of KmCR. A number of variants with improved enzymatic activities were obtained. Among them, the variant KmCR_A100S exhibited increased catalytic efficiency (k(cat)/K-M = 47.3 s(-1)center dot mM(-1)), improved stereoselectivity (from moderate selectivity (de(P) = 66.7%) to strict (S)-selectivity (de(P )> 99.5%)), and extended substrate scope, compared to those of KmCR_WT. In silico analysis showed that a relay system was rebuilt in KmCR via the beneficial residue S100. Furthermore, comparison of 11 protein engineering campaigns indicated that the beneficial position is easily overlooked due to the long distance (>10 angstrom) from ketone substrates. Since CRs share similar catalytic mechanism, the knowledge gained from this study has universal significance to CR engineering.

Automated summary

Enzyme engineering towards catalytic-tetrad residues often leads to activity loss, but a directed evolution campaign on carbonyl reductase KmCR resulted in a beneficial residue A100, leading to variants with improved enzymatic activities. The KmCR variant KmCR_A100S exhibited increased catalytic efficiency, improved stereoselectivity, and extended substrate scope compared to the wild-type KmCR. This study's findings have universal significance to carbonyl reductase engineering.