Saiardi et al. (Saiardi, A., Erdjument-Bromage, H., Snowman, A., Tempst, P., and Snyder, S. H. (1999) Curr. Biol. 9, 1323-1326) previously described the cloning of a kinase from yeast and two kinases from mammals (types 1 and 2), which phosphorylate inositol hexakisphosphate (InsP 6 ) to diphosphoinositol pentakisphosphate, a "high energy" candidate regulator of cellular trafficking. We have now studied the significance of InsP 6 kinase activity in Saccharomyces cerevisiae by disrupting the kinase gene. These ip6k⌬ cells grew more slowly, their levels of diphosphoinositol polyphosphates were 60 -80% lower than wild-type cells, and the cells contained abnormally small and fragmented vacuoles. Novel activities of the mammalian and yeast InsP 6 kinases were identified; inositol pentakisphosphate (InsP 5 ) was phosphorylated to diphosphoinositol tetrakisphosphate (PP-InsP 4 ), which was further metabolized to a novel compound, tentatively identified as bisdiphosphoinositol trisphosphate. The latter is a new substrate for human diphosphoinositol polyphosphate phosphohydrolase. Kinetic parameters for the mammalian type 1 kinase indicate that InsP 5 (K m ؍ 1.2 M) and InsP 6 (K m ؍ 6.7 M) compete for phosphorylation in vivo. This is the first time a PP-InsP 4 synthase has been identified. The mammalian type 2 kinase and the yeast kinase are more specialized for the phosphorylation of InsP 6 . Synthesis of the diphosphorylated inositol phosphates is thus revealed to be more complex and interdependent than previously envisaged.The very dynamic turnover of the "high energy" diphospho- For example, PP-InsP 5 represents the most potent known inhibitor of AP180-mediated assembly of clathrin cages, a key step in the endocytic retrieval of discharged synaptosomal vesicles (2). Other proteins that participate in intracellular trafficking can bind PP-InsP 5 very tightly, including coatomer (3, 4) and AP2 (5). The high affinity with which PP-InsP 5 binds to myelin proteolipid protein may be important for the vesicular delivery of the latter to the myelin sheath (6).Prior experiments with intact cells have shown that Ins(1,3,4,5,6)P 5 and InsP 6 serve as metabolic stockpiles for the formation of the diphosphorylated inositol polyphosphates (7,8). InsP 6 is the precursor for PP-InsP 5 , which is further phosphorylated to [PP] 2 -InsP 4 (5, 7-10). These reactions appear to take place within a metabolic pool that is separate from that in which Ins(1,3,4,5,6)P 5 and PP-InsP 4 are interconverted (7). Thus, there are two metabolic pools of inositol diphosphates that are turned over in parallel cycles.There are increasing efforts to characterize the activities of the enzymes that regulate the turnover of PP-InsP 4 , PP-InsP 5 , and [PP] 2 -InsP 4 . Several phosphatases (diphosphoinositol polyphosphate phosphohydrolases) that hydrolyze these compounds have been described (11,12). Two forms of InsP 6 kinase (types 1 and 2), derived from distinct genes, have been cloned from mammals (13,14). At least in mammals, the further phosphorylati...