To elucidate the structure, tissue-specific expression, and allosteric properties of phosphofructokinase-C (PFK-C), we cloned the cDNA for PFK-C from a rat hypothalamic cDNA library. The cDNA is 2643 base pairs long and encodes a protein of 765 amino acids. The deduced amino acid sequence is highly homologous to PFK-M (muscle) and PFK-L (liver), 69 and 65% amino acid identity, respectively, especially at substrate binding and catalytic sites, while the allosteric binding sites are less conserved. Tissue-specific expression of PFK-C was investigated by Northern blot analysis. PFK-C mRNA was detected in several brain regions and the anterior pituitary but not in liver, skeletal muscle, or several other tissues. In situ hybridization showed that PFK-C is expressed at a higher level in higher brain regions such as the cortex, compared with the midbrain and basal ganglia, while PFK-L is expressed at approximately equal levels throughout the brain. Expression plasmids containing PFK-C and PFK-L coding sequences were constructed and expressed by transient transfection into CMT cells. Expression of transfected PFKs was demonstrated by PFK enzymatic activity and by Western blotting with anti-rat brain and liver PFK antisera. Allosteric regulatory properties of PFK-C and PFK-L expressed in CMT cells were compared. Fructose 2,6-bisphosphate, a potent activator of PFK, decreased the Km of PFK-C for fructose 6-phosphate from 200 to 60 microM while decreasing that of PFK-L from 300 to 55 microM. The properties of PFK-C and PFK-L expressed in CMT cells clearly demonstrate the allosteric differences between the different PFK isozymes.