The expression of atypical zeta-protein kinase C (PKC) was examined during prenatal and postnatal rat brain development. Immunoblot as well as transcript analysis revealed a dramatic increase in expression at 2-3 days post-birth, which declined thereafter and remained at levels observed in the adult brain. The expression of zeta-PKC precedes that of the other PKC isoforms in developing rat brain. Subcellular fractionation of pup and adult brain documented distribution between all three distinct fractions (A,B,C), including the low speed pellet composed of nuclei. In adult brain, the kinase was enriched in the A fraction of the sucrose gradient. Specific substrate proteins of zeta-PKC were characterized in each of the subcellular fractions from both pup and adult brain. Four predominant proteins pp76, pp60-doublet, pp54 and pp45 were identified as zeta-PKC endogenous substrates. All four proteins were phosphorylated on serine residues, while the pp60-doublet was also phosphorylated on tyrosine. The pp60-doublet was the most predominant substrate, specifically enriched in the A fraction of a sucrose gradient of adult brain and immunoprecipitated by monoclonal antibody to pp60c-src.