The immunosuppressant rapamycin prevents cell cycle progression in several mammalian cell lines and the yeast Saccharomyces cerevisiae. In mammalian cells, rapamycin binds to the small FK506-binding protein, FKBP12, allowing the drug-receptor complex to interact with the 289-kDa RAFT1/FRAP proteins. These proteins, along with their yeast homologs, TOR1/DRR1 and TOR2/ DRR2, contain a C-terminal domain with amino acid homology to several phosphatidylinositol (PI) 4-and 3-kinases. However, no direct demonstration of kinase activity for this family of proteins has been reported. We now show that RAFT1, immunoprecipitated from rat brain and MG63 and HEK293 cells, contains PI 4-kinase activity and that rapamycin-FKBP12 has no effect on this activity. Thus, it is likely that, in vivo, rapamycin does not directly inhibit the PI 4-kinase activity and affects the RAFT1/FRAP protein through another mechanism.The ability of rapamycin, a potent immunosuppressant drug, to arrest a variety of mammalian cells and the yeast Saccharomyces cerevisiae in the G 1 stage of the cell cycle (1-4) has made it a valuable tool for studying the intermediate signaling events that convey mitogenic stimuli to the cell nucleus.Rapamycin binds with low nanomolar affinity to the FK506-binding protein (FKBP12), a small soluble protein that is also the intracellular receptor for FK506, a structurally similar immunosuppressant (5-7). Analogous to the mechanism of action of FK506, it is the drug-receptor complex that mediates the effects of the rapamycin, which include inhibition of the 70-kDa S6 kinase (8, 9) and of several cyclin-dependent kinases (2-4). The immunosuppressant effects of FK506 derive from the binding of the FK506-FKBP12 complex to the calcium-activated phosphatase, calcineurin, and the resulting inhibition of its activity (10). Although rapamycin binds to FKBP12, the complex does not interact with calcineurin. Instead, rapamycin-FKBP12 binds to a recently purified and molecularly cloned protein designated rapamycin and FKBP12 target-1 (RAFT1) in rats (11) and FKBP-rapamycin-associated protein (FRAP) in humans (12). Several other groups have subsequently purified and/or cloned the same protein (13-15).RAFT1 is a 2549-amino acid protein with a predicted molecular mass of 289 kDa and is thought to be a mammalian homolog of the products of two yeast genes, TOR1/DRR1 and TOR2/DRR2, which when mutated lead to dominant rapamycin resistance in yeast (1, 16, 17). The C-terminal 600-amino acid domain of RAFT1 and the yeast TOR proteins has homology to several PI 1 kinases, including the p110 subunit of mammalian PI 3-kinase (18); the yeast PI 3-kinase VPS34 (19); two yeast PI 4-kinases, STT4 (20) and PIK1 (21, 22); and the recently cloned mammalian PI 4-kinase, PI4K␣ (23). This homology to known lipid kinases has lead to the suggestion that RAFT1 may also be a PI kinase and that rapamycin exerts its effects by inhibiting this activity (11). However, no direct demonstration of kinase activity for RAFT1/FRAP or the yeast TOR proteins has been r...