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Online Journal of Bioinformatics ©
Volume 12(2):413-430, 2011.
In Silico substrate specificity in bmgt1 and bmgt2 genes of Bacopa monniera glycosyltransferases.
Sharma R, Ruby Zargar, Khan BM, Suresh CG.
Division of Biochemical Sciences and Plant Tissue Culture Division, National Chemical Laboratory, Pune, India
Sharma R, Ruby Z, Khan BM, Suresh CG., In Silico substrate specificity in bmgt1 and bmgt2 genes of Bacopa monniera glycosyltransferases, Onl J Bioinform., 12(2):413-430, 2011. Sequence analysis, structure prediction and docking for glycosyltransferases coded by the bacopa monnieri genes bmgt1 and bmgt2 is described. Molecular structures were modeled by comparative modeling and energy minimization. Bmgt1 had secondary structure elements 12 á-helices and 10 â-sheets and bmgt2, 15 á-helices and 12 â-sheets. The root mean square deviation (RMSD) between modeled structures and corresponding templates was ~1 Å. Docking studies using various acceptor and donor molecules have shown that the structurally conserved Cterminal domain binds the donor molecule and the highly variable N-terminal domain, which can accept a range of molecules, binds the acceptor molecule. The differences between the structures of bmgt1 and bmgt2, their specificities and interactions with various ligands were analyzed. A histidine in the N-terminal domain, conserved throughout the GT families, is a key residue that interacts with the acceptor molecule. Several residues of the highly conserved motif called “plant secondary product glycosyltransferse (PSPG)” that interact with the donor molecule might determine the specificity of enzyme for particular sugar donor. Modeling studies show that a Trp in bmgt1 and Arg in the same position of bmgt2 of PSPG motif may play a role in deciding the sugar specificity of these two enzymes.
Keywords: Docking; Energy minimization; Glycosyltransferase; UDP-Glucose; UDP-Glucuronic acid; Wide specificity