Inhibition of the two-subsite β-d-xylosidase from Selenomonas ruminantium by sugars: Competitive, noncompetitive, double binding, and slow binding modes

The active site of the GH43 β-xylosidase from Selenomonas ruminantium comprises two subsites and a single access route for ligands. Steady-state kinetic experiments that included enzyme (E), inhibitory sugars (I and X) and substrate (S) establish examples of EI, EII, EIX, and EIS complexes. Protonation states of catalytic base (D14, pKa 5) and catalytic acid (E186, pKa 7) govern formation of inhibitor complexes and strength of binding constants: e.g., EII, EIX, and EIS occur only with the D14−E186H enzyme and d-xylose binds to D14−E186− better than to D14−E186H. Binding of two equivalents of l-arabinose to the D14−E186H enzyme is differentiated by the magnitude of equilibrium Ki values (first binds tighter) and kinetically (first binds rapidly; second binds slowly). In applications, such as saccharification of herbaceous biomass for subsequent fermentation to biofuels, the highly efficient hydrolase can confront molar concentrations of sugars that diminish catalytic effectiveness by forming certain enzyme-inhibitor complexes.