Figure 5
Model of SYDE1 and SYDE2 RhoGAP domain complexed with RhoA. RhoGAP domains of SYDE1 (a) and SYDE2 (b) bound to RhoA, and SYDE1 RhoGAP (c) bound to RhoB were modeled by SwarmDock program. Structure of MgcRacGAP/RhoA complex is shown (d). Conserved regions consist of arginine finger (red dotted circle), positively charged interface (purple dotted oval) and hydrophilic interface (orange dotted oval) in RhoGAP domains face to switch II (orange oval) and P-loop (red circle) of RhoA are indicated. Predicted structure of the substrate recognition sites specifically interacting with P-loop and Switch I and II are indicated (e–g). The side-chains of the conserved residues among the RhoGAPs are shown on the cartoon (e–g). (e) Arginine finger locates between second and third α-helices and cysteine and arginine tether to the interface formed by glycine and glutamic acid of RhoA or RhoB (red-edged circles). (f) Each modeled arginine finger in the RhoGAP complex with RhoA or RhoB is superimposed to the corresponding region of MgcRacGAP structure (PDB: 5c2k). RhoGAP domains of SYDE1/2 and MgcRacGAP are shown as the gold and light blue, respectively. The bound-RhoGTPases to SYDE1/2 and MgcRacGAP are colored as green and pink, respectively. (g) RhoGAP domain and P-loop and SwitchI/II region of RhoGTPases are colored as gold and green, respectively. Side chains of the conserved positively charged residues and conserved residues organizing hydrophilic regions show similar orientation on the ternary helical structure to the corresponding residues of the template by forming the Rho binding interfaces. Cartoon of each model was manually retrieved and indicated as colored molecules separately from the predicted docking structure by Chimera software.
