Structural evidence of a phosphoinositide-binding site in the Rgd1-RhoGAP domain

Phosphoinositide lipids recruit proteins to the plasma membrane involved in the regulation of cytoskeleton organization and in signalling pathways that control cell polarity and growth. Among those, Rgd1p is a yeast GTPase activating protein (GAP) specific for Rho3p and Rho4p GTPases, which control actin polymerization and stress signalling pathways. Phosphoinositides not only bind Rgd1p, but also stimulate its GAP activity on the membrane-anchored form of Rho4p. Both F-BAR and RhoGAP domains of Rgd1p are involved in lipid interactions. In the Rgd1p-F-BAR domain, a phosphoinositide binding site has been recently characterized. We report here the X-ray structure of the Rgd1p-RhoGAP domain, identify by NMR spectroscopy and confirm by docking simulations, a new but cryptic phosphoinositide binding site, comprising contiguous A1, A19 and B helices. The addition of helix A19, unusual among RhoGAP domains, seems to be crucial for lipid interactions. Such a site was totally unexpected inside a RhoGAP domain, as it was not predicted from either the protein sequence or its three-dimensional structure. Phosphoinositide binding sites in RhoGAP domains have been reported to correspond to polybasic regions (PBR), which are located at the unstructured flexible termini of proteins. Solid state NMR spectroscopy experiments confirm the membrane interaction of the Rgd1p-RhoGAP domain upon addition of PtdIns(4,5)P 2 and indicate a slight membrane destabilization in the presence of the two partners.