Homology modelling and docking studies of strictosidine β-D-glucosidase from Madagascar periwinkle (Catharanthus roseus Bunge)
by Piotr Szymczyk; Grażyna Szymańska; Małgorzata Majewska; Izabela Weremczuk-Jeżyna; Michał Kołodziejczyk; Kamila Czarnecka; Paweł Szymański; Ewa Kochan
International Journal of Bioinformatics Research and Applications (IJBRA), Vol. 18, No. 3, 2022

Abstract: Here, the structure of the enzyme and substrate binding site of C. roseus strictosidine β-D-glucosidase is reported. An homology model of C. roseus strictosidine β-D-glucosidase was built using the Discovery Studio 4.1 software package and rice Os3bglu6 β-glucosidase (PDB code: 3GNPA) as a template. The CDOCKER algorithm was used to dock the natural substrate, strictosidine, as well as an inhibitor D-glucono 1,5-lactone. Obtained structures were refined in the course of molecular dynamic simulation. Analysis of the acquired data provided information on the C. roseus strictosidine β-D-glucosidase amino acid residues interaction with the natural substrate and inhibitor. Our findings expand the basic knowledge of the structure of the C. roseus strictosidine β-D-glucosidase active site, and may also be used in the design of enzyme point mutations with improved stability and catalytic properties, or to change substrate specificity.

Online publication date: Mon, 22-Aug-2022

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