Molecular insights into the membrane-associated phosphatidylinositol 4-kinase IIα

Phosphatidylinositol 4-kinase II alpha (PI4KII alpha), a membrane-associated PI kinase, plays a central role in cell signalling and trafficking. Its kinase activity critically depends on palmitoylation of its cysteine-rich motif (-CCPCC-) and is modulated by the membrane environment. Lack of atomic structure impairs our understanding of the mechanism regulating kinase activity. Here we present the crystal structure of human PI4KIIa in ADP-bound form. The structure identifies the nucleotide-binding pocket that differs notably from that found in PI3Ks. Two structural insertions, a palmitoylation insertion and an RK-rich insertion, endow PI4KIIa with the 'integral' membrane-binding feature. Molecular dynamics simulations, biochemical and mutagenesis studies reveal that the palmitoylation insertion, containing an amphipathic helix, contributes to the PI-binding pocket and anchors PI4KIIa to the membrane, suggesting that fluctuation of the palmitoylation insertion affects PI4KII alpha's activity. We conclude from our results that PI4KIIa's activity is regulated indirectly through changes in the membrane environment.