Catalyzes the dehydration of D-xylonic acid to form 2-dehydro-3-deoxy-D-pentonate. D-xylonate = 2-dehydro-3-deoxy-D-arabinonate + H2O Expression is repressed by the transcriptional regulator XynR. 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.