Mapping secondary substrate‐binding sites on the GH11 xylanase from Bacillus subtilis

Xylanases are of significant interest for biomass conversion technologies. Here, we investigated the allosteric regulation of xylan hydrolysis by the Bacillus subtilis GH11 endoxylanase. Molecular dynamics simulations (MDS) in the presence of xylobiose identified binding to the active site and two potential secondary binding sites (SBS) around surface residues Asn54 and Asn151. Arabinoxylan titration experiments with single cysteine mutants N54C and N151C labeled with the thiol‐reactive fluorophore acrylodan or the ESR spin‐label MTSSL validated the MDS results. Ligand binding at the SBS around Asn54 confirms previous reports, and analysis of the second SBS around N151C discovered in the present study includes residues Val98/Ala192/Ser155/His156. Understanding the regulation of xylanases contributes to efforts for industrial decarbonization and to establishing a sustainable energy matrix. Ligand binding to secondary binding sites modulates GH11 endo‐1,4‐β‐xylanase activity towards hemicellulose. In this study, predicted substrate binding to the active site (light gray) and two product‐binding subsites (light blue and yellow) of the Bacillus subtilis enzyme were confirmed experimentally. This understanding of GH11 regulation has implications for the enzymatic saccharification of lignocellulosic biomass for the circular economy.