QM/MM study of catalytic mechanism of Xylanase Cex from Cellulomonas fimi

Xylanase Cex from Cellulomonas fimi is a bifunctional enzyme that catalyzes the degradation of both cellulose and xylan. As a result, it might find valuable applications in production of biofuels. In this work, we presented a detailed theoretical investigation of hydrolysis of the xylopentaose molecule catalyzed by Cex, using a hybrid quantum mechanical and molecular mechanical approach. Our results support the experimental observation that the hydrolysis proceeds via the net retention mechanism. More interestingly, our simulations indicate that the xylose unit at −1 binding site should take a boat (B2,5) conformation as a possible reactive conformer, while the oxo-carbenium ion-like transition states take the combination of B2,5/OS2 for glycosylation, and OS2/O,3B for deglycosylation. Our molecular dynamics simulations of mutants further suggest that two catalytic residues (E127 and E233) play the vital role in this ring distortion. Indeed, this conformational change is necessary to facilitate the first step of nucleophilic attack by E233 at the anomeric carbon center.

Graphical abstractFigure optionsDownload full-size imageDownload high-quality image (73 K)Download as PowerPoint slideHighlights► Catalytic mechanism was analyzed for Xylanase using SCC-DFTB/MM method. ► Two dimensional potentials of mean force were computed for the hydrolysis reaction. ► The substrate distortion mechanism was suggested to be induced by protein environment.