Phosphatidylinositol 4-kinase II (PI4KII), the most abundant PI4K in mammalian cells, is best known for its essential role in providing the substrate for phosphatidylinositol 3-kinase (PI3K), an important kinase for phospholipid signaling. PI4KII also plays important roles in membrane trafficking, phagocytosis and the exo-endocytic cycle of synaptic vesicles. Its dysfunction results in tumor growth, spastic paraplegia and Gaucher's disease. Therefore, PI4KII may potentially be an important drug target.The PI4K family comprises type II (55 kD PI4KII and PI4KIIβ) and type III PI4Ks (230 kD PI4KIIIand 92 kD PI4KIIIβ). Phylogenetic analysis [1] based on their sequences ( Figure 1A) reveals that PI4KIIIs are closed to PI3Ks thus belong to the PI 3/4-kinase family while PI4KIIs have more closed relationship with protein kinases (e.g., Actin fragmin kinase). This suggests that PI4KIIs should have a substrate binding pocket that is distinct from that of PI3Ks and PI4KIIIs. In addition, PI4KII contains a '-CCPCC-' motif that is palmitoylated in vivo and such palmitoylation is important for the kinase activity of PI4KII. Thus currently structural information available on PI3Ks and the well-developed specific PI3K inhibitors are not helpful for understanding the substrate binding specificity and the activity regulation of PI4KIIs.Recently, the first crystal structure in the PI4K family, the catalytic domain of human PI4KII in an ADP-bound form was solved [2], and three novel insertions of PI4KII, namely I1 (a palmitoylation insertion), I2 (an RK-rich insertion) and I3 were found in this crystal structure ( Figure 1B). These three insertions distinguish PI4KII from the structures of PI3Ks ( Figure 1C). Furthermore, a distinct nucleotide-binding pocket of PI4KII differs notably from that of PI3Ks, which well explained the insensitivity of PI4KII to PI3Ks' inhibitors. Although many crystal structures of PIKs have already been solved, the precise nature of the substrate binding pocket is still not clear. The molecular dynamics (MD) simulation approach was utilized to identify a putative PI-binding pocket that was further evaluated using mutagenesis. More importantly, the MD simulation, biochemical and mutagenesis studies revealed a novel mechanism for the regulation of PI4KII's kinase activity, in which any perturbation of the interaction between PI4KII and the membrane will affect either the nucleotide binding or PI binding and subsequently modulate the kinase activity of PI4KII.Current work [2] has provided insight into how the kinase activity of PI4KII is regulated at the molecular level. It also lays a foundation for designing specific PI4KII inhibitors and activators for future therapeutic applications. Importantly, it brings PI4KII out of the shadow of PI3K and sheds new light on the study of PI4KII in its own rite. Future studies could be focused on the following directions: (i) Discovery of specific inhibitors based on the ADP binding pocket of PI4KII PI4KII has been proved as an oncoprotein and...