A protein has been purified from rat liver (about 5 mg from 100 g) which inactivates rat liver phosphofructokinase-1. According to dodecyl sulfate gel electrophoresis the protein consists of a single peptide chain with a Mr of 19,000. The inactivation of phosphofructokinase-1 by this protein results from a dissociation of phosphofructokinase-1 into its inactive protomers (Mr = 82,000). The inactivation is dependent on zinc ions in micromolar concentration (about 1-2 microM), but is inhibited by higher concentrations (greater than 50 microM). Fructose 1,6-bisphosphate as well as fructose 2,6-bisphosphate inhibit the inactivation reaction. In addition, both compounds as well as ATP can reverse the dissociation of phosphofructokinase-1. The phosphofructokinase-1 inactivating protein has no phosphatase activity with [32P]phosphofructokinase or low molecular weight phospho-compounds and does not possess any detectable proteolytic activity. It has the same affinity for the phospho- and the dephosphoform of phosphofructokinase-1, but preincubation of phosphofructokinase-1 with this inactivating protein reduces the maximum amount of phosphate incorporated into phosphofructokinase-1 and accelerates the velocity of the dephosphorylation reaction. A direct Zn2+-dependent binding of phosphofructokinase-1 to the inactivating protein has been demonstrated in experiments with matrix-bound phosphofructokinase-1 inactivating protein.