The expression of a high affinity Na(+)- (and Cl-) dependent L-proline transporter (PROT) in subpopulations of putative glutamatergic pathways in rat brain raises the possibility of a specific physiological role(s) for this carrier in excitatory neurotransmission (Fremeau, R. T., Jr., Caron, M. G., and Blakely, R. D. (1992) Neuron 8, 915-926). However, the biochemical properties and regional, cellular, and subcellular distribution of the PROT protein have yet to be elucidated. Here, we document the brain-specific expression and neuronal localization of rat PROT mRNA. We also report the first identification and partial biochemical characterization of the mammalian brain PROT protein. An affinity-purified antipeptide antibody was produced that specifically recognized a single 68-kDa PROT protein on immunoblots of rat and human brain tissues. Deglycosylation of rat hippocampal membranes with peptide-N-glycosidase F reduced the apparent molecular mass of the native PROT protein from 68 to 53 kDa, the size of the primary PROT translation product determined by in vitro translation of the rat PROT cDNA in the absence of microsomes. Subcellular fractionation studies demonstrated that the PROT protein was enriched in synaptic plasma membranes but absent from postsynaptic densities. A differential distribution of PROT mRNA and protein was observed in rat striatum, suggesting that the transporter protein is synthesized in neuronal cell bodies in the cortex and exported to axon terminals in the caudate putamen. These findings warrant the consideration of a novel presynaptic regulatory role for this transporter in excitatory synaptic transmission.