Molecular Simulation and Catalytic Active Sites Identification of Dammarenediol-II Synthase

Squalene and oxidosqualene cyclizations are regarded as the most complex chemical reactions in the nature, which can achieve protonation, deprotonation,a sequence of hydride and methyl migration. Dammarenediol-Ⅱ synthase (DS), as a kind of 2,3-oxidosqualene-triterpene cyclase, catalyses 2,3-oxidosqualene to form dammarenediol-Ⅱ. To assess the three-dimensional (3D) structure and catalytic active sites of dammarenediol-Ⅱ synthase, utilizing the homology modeling method, 3D models of DS were established in the Modeller9v14 software and I-TASSER server. With the highest sequence identity with DS, human oxidosqualene cyclase 3D models (PDB:1W6K and 1W6J) were chosen as templates. Through further evaluation and optimization, an optimal DS model was obtained consequently. Then several putative catalytic active sites were found through the molecular docking simulation between DS model and product dammarenediol-Ⅱ by using Autodock 4.2. Finally, site-directed mutants of DS were expressed in Saccharomyces cerevisiae, a significant decrease of the yield of dammarenediol-Ⅱ is achieved, which verified the significance of these putative active sites.