Catalyzes the dehydration of D-xylonic acid to form 2-dehydro-3-deoxy-D-pentonate. D-xylonate = 2-dehydro-3-deoxy-D-arabinonate + H2O Activity is increased in the presence of Mn(+) and Mg(2+). Inhibited by thiol compounds. kcat is 0.33 min(-1). Optimum pH is 8.0. Optimum temperature is 30 degrees Celsius. Disruption mutant has reduced ability to catabolize D-xylonic acid. YjhG-yagF double mutant cannot use D-xylonate as the sole source of carbon. Belongs to the IlvD/Edd family.