Pm. Coutinho et al., AUTOMATED DOCKING OF ALPHA-(1,4)-LINKED AND ALPHA-(1,6)-LINKED GLYCOSYL TRISACCHARIDES IN THE GLUCOAMYLASE ACTIVE-SITE, Industrial & engineering chemistry research, 37(6), 1998, pp. 2148-2157
Low-energy conformers of five alpha-(1,4)- and alpha-(1,6)-linked gluc
osyl trisaccharides were flexibly docked into the glucoamylase active
site using AutoDock 2.2. To ensure that all significant conformational
space was searched, the starting trisaccharide conformers for docking
were all possible combinations of the corresponding disaccharide low-
energy conformers. All docked trisaccharides occupied subsites -1 and
+1 in very similar modes to those of corresponding nonreducing-end dis
accharides. For linear substrates, full binding at subsite +2 occurred
only when the substrate reducing end was alpha-(1,4)-linked, with hyd
rogen-bonding with the hydroxymethyl group being the only polar intera
ction there. Given the absence of other important interactions at this
subsite, multiple substrate conformations are allowed. For the one do
cked branched substrate, steric hindrance in the alpha-(1,6)-glycosidi
c oxygen suggests that the active-site residues have to change positio
n for hydrolysis to occur. Subsite +1 of the glucoamylase active site
allows flexibility in binding but, at least in Aspergillus glucoamylas
es, subsite +2 selectively binds substrates alpha-(1,4)-linked between
subsites +1 and +2. Enzyme engineering to limit substrate flexibility
at subsite +2 could improve glucoamylase industrial properties.