Template-based modeling of a psychrophilic lipase: Conformational changes, novel structural features and its application in predicting the enantioselectivity of lipase catalyzed transesterification of secondary alcohols

In order to fully explore the structure–function relationship of a Proteus lipase (LipK107) that was screened from the soil in our previous study, we have modeled the three-dimensional (3-D) structures of the enzyme in its active and inactive conformations on the basis of crystal structures of Burkholderia glumae and Pseudomonas aeruginosa lipases in the present study. Both homology models suggested that LipK107 possessed a catalytic triad (Ser79–Asp232–H254), an oxyanion hole (Leu13 and Gln80) which was used to stabilize the reaction tetrahedral intermediates, and a lid substructure that controlled the access of the substrate to the active site. The existence of the lid was further verified by carrying out the interfacial activation experiment. The conformational change of LipK107 which was caused by lid opening action was predicted by superimposing the two theoretical models for the first time. Finally, both 3-D structures were used to predict the enantioselectivity of LipK107 when the enzyme was used to catalyze the resolution of racemic 1-phenylethanol. Lid-open model of LipK107 identified the R-enantiomer as the preferred enantiomer, while lid-closed mode showed that the S-enantiomer was more favored. However, only the lid-open conformational model could led to predictions that agreed with the following the experimental result of real biocatalysis reaction of 1-phenylethanol.

Research Highlights
► Contrary to other modeling researches, two models (lid-open and lid-closed conformation) of LipK107 were built, and both models identified the same key structural features of the lipase. This guaranteed the accuracy modeling results.
► In contrast to other modeling papers, experimental means were applied to verify structural features (the lid substructure) identified by homology models.
► Superimposing the two static models predicted a dynamic view of lid opening action.
► Both models were used to predict the enantioselectivity of the lipase by molecular dynamics simulation, and the predicting results were in agreement with the experimental results.
► LipK107 was originally discovered by our group. Gao et al, J Biotech. 139 (2009) 169-175.