Enzymatic characterization and docking simulation of a xylan synthase catalytic subunit, <i>Setaria viridis</i> IRX10, using xylotrimer acceptors with distinct fluorescent labels

Arabinoxylan, a major hemicellulose in plant cell walls, particularly in grasses and cereals, plays a crucial role in structural integrity and biological functions, with diverse industrial applications such as food production and prebiotic development. Despite its significance, the molecular mechanism of arabinoxylan biosynthesis remains unclear. Here, we identified and characterized a xylan synthase catalytic subunit, <i>Setaria viridis</i> IRregular Xylem 10 (SvIRX10), from a new model plant for C₄-photosynthetic grasses, <i>S. viridis</i> A10.1. Bioinformatic analysis classified SvIRX10 as a glycosyltransferase 47 family member, conserved across various species. Recombinant SvIRX10 expressed in Expi293 cells exhibited xylan synthase activity for all tested xylotrimer (Xyl₃) acceptors with distinct fluorescent labels. The substrate conversion efficiency for 2-aminobenzoic acid-labeled Xyl₃ (Xyl₃-2AA) was highest, but those for other labeled Xyl₃ were lower. Nevertheless, the elongation efficiencies were comparable among tested acceptors when the xylan chains elongated enough. Structural prediction and docking simulations illustrated most frequently the productive conformations using Xyl₃-2AA and xylotetraose as ligands. The interactions between the two ligands and the active site were well-conserved, and all ligand units interacted with SvIRX10. These ligand conformations in the active site were similar, but those of other fluorescently labeled Xyl₃ differed except for the first xylosyl unit at the non-reducing end. Thus, SvIRX10 recognizes at least 4 xylosyl units in the xylan synthetic reaction. Together, these findings provide insights into the enzymatic mechanisms of SvIRX10 and the initiation of xylan elongation, offering potential applications for modifying plant cell walls in biomass utilization and functional food development.