The catalytic subunits of protein kinase A are transcribed in all mouse tissues from two distinct genes that code for the C alpha and C beta isoforms. Alternative promoters exist for the C beta gene that are used in a tissue-specific fashion and give rise to variants that differ in their amino-terminal sequences. We have characterized an alternative promoter that is present in the first intron of the C alpha gene and is transcriptionally active in male germ cells. Transcription from this promoter is coincident with the appearance of pachytene spermatocytes and leads to a C alpha protein (C alpha 2) that contains a distinctive 7 amino acid amino-terminus differing from the 14 amino acid amino-terminus of C alpha 1. The C alpha 2 protein does not contain the myristylation signal present on coil and migrates at a lower molecular weight on SDS/PACE gels. By Western blotting, we estimate that most or all of the C alpha protein present in mature sperm is C alpha 2. The amino-terminal sequence of C alpha 2 is similar to that of ovine sperm C as previously reported [San Agustin, J. T., Leszyk, J. D., Nuwaysir, L. M. & Witman, G. B. (1998) J. Biol. Chem. 273, 24874-24883], and we show by cDNA cloning that human sperm also express a highly related C alpha 2 homolog. The C alpha 2 subunit forms holoenzymes with either RII alpha or RI alpha, and both activate at the same concentration of cyclic nucleotide. Because protein kinase A is thought to play a pivotal role in sperm motility and capacitation, the distinctive biochemical properties of the unmyristylated C alpha 2 may be essential for fertility in the male.