Figure 4
Structural features associated with co-conserved residues that are distinctive of Arf/Arl/Sar GTPases and that form a network of salt bridges. Arf/Arl/Sar GTPases features correspond to column 12 in Fig. 2 and to the contrast alignment in Fig. 3C. See the legend to Fig. 1A for side chain and backbone color schemes. Shown in gray are the side chains of residues at an (unclassified) position within the α3-helix that weakly conserves an acidic amino acid which also participates in the Arf/Arl salt-bridge network. (A) Arf1 + GTP (pdb_id: 1o3y; 1.50 Ǻ)[57]. (B) Arf6 + GTP + Cholera toxin (not shown) (pdb_id: 2a5d; 1.80 Ǻ) [36]. (C) Arl1 + GTP + Golgin-245 Grip domain (not shown) (pdb_id: 1upt; 1.7 Ǻ) [37]. (D) Arl2 + GDP + PO43- and its effector PDE-δ (not shown) (pdb: 1ksh; 1.80 Ǻ) [38]. (E) Arl6 + GTP (pdb_id: 2 h57; 2.00 Ǻ) [Structural Genomics Consortium]. (F) Sar1 GTPase bound to a GTP analog (GppNHp)) and to the GAP protein Sec23 (pdb_id: 1m2o; 2.50 Ǻ) [41]; the side chain of the arginine-finger of Sec23 is shown in gray. (G) Gα bound to RGS4, GDP and AlF4 (transition state structure)(pdb_id: 1agr; 2.8 Ǻ) [58]. The side-chains of three residues that are specifically conserved in Gα subunits[6] (one of which is the arginine finger, Arg178) are shown in blue.