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Mechanism of substrate specificity of phosphatidylinositol phosphate kinases

Significance Phosphatidylinositol phosphate kinases (PIPKs) generate two highly important phosphatidylinositol bisphosphates, PI(4,5)P2 and PI(3,5)P2, which are central to many signaling and membrane trafficking processes. The three types of PIPKs are homologous in sequence but demonstrate different substrate and catalytic specificities. In this study, we provide crystallographic and biochemical evidence showing that the complex pattern of substrate recognition and phosphorylation results from interplay between two structural elements: the specificity loop and the binding site for the monophosphate moiety of the substrate. This work provides the first complete understanding of how this family of lipid kinases achieves exquisite substrate specificity. The mechanistic insights presented are timely because an increasing number of studies implicate lipid kinases in major human diseases, including cancer and diabetes. The phosphatidylinositol phosphate kinase (PIPK) family of enzymes is primarily responsible for converting singly phosphorylated phosphatidylinositol derivatives to phosphatidylinositol bisphosphates. As such, these kinases are central to many signaling and membrane trafficking processes in the eukaryotic cell. The three types of phosphatidylinositol phosphate kinases are homologous in sequence but differ in catalytic activities and biological functions. Type I and type II kinases generate phosphatidylinositol 4,5-bisphosphate from phosphatidylinositol 4-phosphate and phosphatidylinositol 5-phosphate, respectively, whereas the type III kinase produces phosphatidylinositol 3,5-bisphosphate from phosphatidylinositol 3-phosphate. Based on crystallographic analysis of the zebrafish type I kinase PIP5Kα, we identified a structural motif unique to the kinase family that serves to recognize the monophosphate on the substrate. Our data indicate that the complex pattern of substrate recognition and phosphorylation results from the interplay between the monophosphate binding site and the specificity loop: the specificity loop functions to recognize different orientations of the inositol ring, whereas residues flanking the phosphate binding Arg244 determine whether phosphatidylinositol 3-phosphate is exclusively bound and phosphorylated at the 5-position. This work provides a thorough picture of how PIPKs achieve their exquisite substrate specificity.