Studies of in vitro phosphorylation of four different gluconeogenic fructose-1,6-bisphosphatases by the catalytic subunit of cyclic AMP-dependent protein kinase have shown that only rat liver fructose-1,6-bisphosphatase is a substrate of the protein kinase. A comparison of the molecular weights of fructose-1,6-bisphosphatases revealed that the nonphosphorylatable mouse liver, rabbit liver, and pig kidney enzymes have a subunit Mr approximately 37,000 while the subunit molecular weight of purified rat liver fructose-1,6-bisphosphatase is about 41,000 (Hosey, M. M., and Marcus, F. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 91-94). To probe the structural basis for the higher molecular weight and unique phosphorylation of rat liver fructose-1,6-bisphosphatase, the CNBr fragment containing the phosphorylation site was purified and the amino acid sequence of this 43-residue peptide was determined. The sequence data revealed that the rat liver enzyme extends 24-26 residues beyond the COOH-terminal amino acid of pig kidney and rabbit liver fructose-1,6-bisphosphatase and that cyclic AMP-dependent phosphorylation sites are located in this proline-rich extension. The kinetic properties of rat liver fructose-1,6-bisphosphatase do not appear to be influenced in any way, either by the COOH-terminal extension itself or by the state of phosphorylation. Polyacrylamide gel electrophoresis of immunoprecipitates from crude extract supernatants demonstrated that the rat liver enzyme is larger than other fructose-1,6-bisphosphatases studied to date, and that the differences in molecular weight are not due to proteolytic modification of other fructose-1,6-bisphosphatases during isolation procedures.