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

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 xylooligosaccharides, 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, +1, +2, and +3. 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 (+1), Tyr88 (+2) and Tyr173 (+3). The bond-cleavage positions showed that X2 and X3 did not bind at the cleft (subsites -1 and +1) 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.