Substrate-binding site of family 11 xylanase from Bacillus firmus K-1 by molecular docking

Abstract

The three-dimensional structure (3D structure) of Xyn11A, a family 11 xylanase from Bacillus firmus K-1, was obtained through homology modeling. To study the substrate-binding site of Xyn11A, six xylooligosacchar-ides, xylobiose to xyloheptaose (X2-X7), were docked into the active site of Xyn11A by molecular docking. Based on the docked energy and estimated free energy of binding combined with modeled enzyme-substrate complexes, the substrate-binding site of Xyn11A probably contained six subsites, defined as -3, -2, - 1, p1, p2, and p3. Focus on possible stacking interaction presented seven aromatic residues, that played an important role in six subsites of Xyn11A such as Tyr165 (-3), Trp9 and Tyr69 (-2), Tyr80 (-1), Tyr65 (p1), Tyr88 (p2) and Tyr173 (p3). The bond-cleavage positions showed that X2 and X 3 did not bind at the cleft (subsites -1 and p1) of Xyn11A. Related to the experiment, the end products of larchwood xylan hydrolysis by purified Xyn11A were X2 and X3. X2 and X3 acted as the end product inhibitors of Xyn11A.