Catalyzes the ATP-dependent phosphorylation of D-fructose 6-phosphate to fructose 1,6-bisphosphate. Together with the adjacently encoded sucrose 6'-phosphate phosphorylase, may be involved in a new pathway for the degradation of sucrose. Cannot phosphorylate D-fructose. ATP + beta-D-fructose 6-phosphate = ADP + beta-D-fructose 1,6-bisphosphate + H(+) Belongs to the carbohydrate kinase PfkB family.