Evolution of a Signaling Nexus Constrained by Protein Interfaces and Conformational States
Figure 5
G(12) class-distinctive sites in structural context.
(A) The structure of the p115RhoGEF RGS-like box domain (dark teal cartoon) and a βN-αN hairpin element (cyan loop cartoon) bound to an activated Gα13/i1 chimera (Gα13/i1•GDP•Mg2+•AlF4−) (PDB ID 1SHZ). In all structural panels in this figure, Gα is shown as spheres with core residues colored gray if they are conserved between Gα subunits (either INV (invariant) or η (non-distinct) amino acids) while G(12)-distinctive sites are colored yellow orange only if they contain a ∂ (distinct) amino acid. The chimeric Gα subunit in this structure also contained ∂ (distinct) amino acids at several G(io)-distinctive sites (green spheres). Non-core residues and d sites are colored white. G(12)-distinctive sites are numbered according to their position in the signature sequence (see panel (D)). (B) Model of Gα12/i1 in complex with p115RhoGEF. Gα is in the same orientation as panel A. (C) Homology model of Gα12•GDP (sphere display) bound to Gβ•Gγ (deep blue/copper cartoon) heterodimer. Two orientations related by a 180° rotation about the vertical axis are shown. The inset is a close up view of the Gβγ binding region in the right view. (D) Signature sequences are formed by grouping all distinctive sites for a given class together, removing all residues between individual distinctive sites of the noted class. The distinctive sites for each class are presented in order from the N-terminus to the C-terminus and numbered accordingly. Amino acids that correspond to the ∂ values at the G(12) site are colored yellow orange. Sites that have direct interactions with p115RhoGEF are denoted by ‘R’ above the site, while additional sites in switches I or II are denoted by ‘1’ or ‘2’, respectively, above the site.