Catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) to produce 2-keto-3-deoxy-6-phosphogluconate (KDPG). 2-dehydro-3-deoxy-D-gluconate + ATP = 2-dehydro-3-deoxy-6-phospho-D-gluconate + ADP + H(+) Carbohydrate acid metabolism; 2-dehydro-3-deoxy-D-gluconate degradation; D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-3-deoxy-D-gluconate: step 1/2. Expression is probably repressed by KdgR, which binds to its 5'-UTR. Belongs to the carbohydrate kinase PfkB family.