Catalyzes the dehydration of 6-phospho-D-gluconate to 2-dehydro-3-deoxy-6-phospho-D-gluconate. 6-phospho-D-gluconate = 2-dehydro-3-deoxy-6-phospho-D-gluconate + H2O Binds 1 [4Fe-4S] cluster. Sensitive to oxidants such as superoxide or hydrogen peroxide. Carbohydrate metabolism; Entner-Doudoroff pathway. By growth on gluconate. The mutant grows at normal rates on glucose and fructose, whereas on gluconate it grows about one-third as fast as the wild-type. Belongs to the IlvD/Edd family.