Abstract
To enhance the specific activity and catalytic efficiency (k cat/K m) of an NADH-dependent LpPPR, its directed modification was performed based on the computer-aided design using molecular docking simulation and multiple sequence alignment. Firstly, five single-site variants of an LpPPR-encoding gene (lpppr) were amplified and expressed in E. coli BL21 (DE3). The asymmetric reduction of 20 mM phenylpyruvic acid (PPA) was carried out using 50 mg/mL E. coli/lpppr R53Q or /lpppr A79V whole wet cells at 37 °C for 20 min, giving d-phenyllactic acid (PLA) with 41.1 or 44.3% yield, being 1.17- or 1.26-fold that by E. coli/lpppr. Secondly, double-site variants were obtained by saturation mutagenesis of Ala79 in LpPPRR53Q. Among all tested E. coli transformants, E. coli/lpppr R53Q/A79V exhibited the highest d-PLA yield of 85.3%. The specific activity and k cat/K m of the purified LpPPRR53Q/A79V increased to 67.5 U/mg and 169.8 mM-1 s-1, which were 3.0- and 13.2-fold those of LpPPR, respectively. Finally, the catalytic mechanism analysis of LpPPRR53Q/A79V by molecular docking simulation indicated that the replacement of Arg53 in LpPPR with Gln expanded its substrate-binding pocket, while that Ala79 with Val formed an additional π-sigma interaction with phenyl group of PPA. Supplementary material: The online version of this article (10.1007/s13205-020-02633-3) contains supplementary material, which is available to authorized users.