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OJBTM
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
ABSTRACT
Sharma R, Ruby Z, Khan BM, Suresh CG., In Silico substrate specificity in
bmgt1 and bmgt2 genes of Bacopa monniera
glycosyltransferases, Online J Bioinformatics,
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