Cryo-EM structures of cancer-specific helical and kinase domain mutations of PI3K alpha

Phosphoinositide 3-kinases (PI3Ks) are a family of lipid kinases that perform multiple and important cellular functions. The protein investigated here belongs to class IA of the PI3Ks; it is a dimer consisting of a catalytic subunit, p110 alpha, and a regulatory subunit, p85 alpha, and is referred to as PI3K alpha. The catalytic subunit p110 alpha is frequently mutated in cancer. The mutations induce a gain of function and constitute a driving force in cancer development. About 80% of these mutations lead to single-amino-acid substitutions in one of three sites of p110 alpha: two in the helical domain of the protein (E542K and E545K) and one at the C-terminus of the kinase domain (H1047R). Here, we report the cryo-electron microscopy structures of these mutants in complex with the p110 alpha-specific inhibitor BYL-719. The H1047R mutant rotates its sidechain to a new position and weakens the k alpha 11 activation loop interaction, thereby reducing the inhibitory effect of p85 alpha on p110 alpha. E542K and E545K completely abolish the tight interaction between the helical domain of p110 alpha and the N-terminal SH2 domain of p85 alpha and lead to the disruption of all p85a binding and a dramatic increase in flexibility of the adaptor-binding domain (ABD) in p110 alpha. Yet, the dimerization of PI3K alpha is preserved through the ABD-p85 alpha interaction. The local and global structural features induced by these mutations provide molecular insights into the activation of PI3K alpha, deepen our understanding of the oncogenic mechanism of this important signaling molecule, and may facilitate the development of mutant-specific inhibitors.