Figure 5

Structural locations of Arf/Arl co-conserved residues. (A-C) Conserved residues (green side-chains) distinguishing Arf/Arl from Sar and Gα GTPases (column 13 in Fig. 2; Fig. 3D). (A) The structure of Arf1 bound to GTP. The region shown corresponds to a β sheet adjacent to the Walker B region. Note that the asparagine of the N-[VI] motif (Asn52) forms a hydrogen bond with the Walker B aspartate (Asp67), whereas the valine (Val53) packs up against a tryptophan (Trp66) that directly precedes the aspartate. An Arf/Arl-conserved isoleucine (Ile74) packs against the backbone connecting the switch I threonine residue (Thr48) to the switch I glycine (Gly50; unlabeled in figure). (B) The structure of Arf1 bound to GDP. Note that the β-strand corresponding to the Walker B "W-D" motif has shifted to the left by two residue positions due to Arf's interswitch toggle and that the N-[VI] motif interactions are disrupted. (C) The structural location of the Arf/Arl conserved glutamine (Gln128) and alanine (Ala125) residues associated with the guanine binding loop (the NK-x-D motif). The glutamine may stabilize this loop by forming hydrogen bonds with backbone oxygen atoms on either side of this loop, as shown. (D-E). Structural locations of residues (blue side-chains) that are conserved in and distinctive of Arl8 GTPases (column 16 in Fig. 2; Fig. S4D in Additional File 1). Residue side chains corresponding to the N-[IV] motif (of Arf/Arl GTPases) are shown in green. Note that Arl8-specific conserved residues form alternative interactions in the two forms, suggesting that they play a role in the interswitch toggle. (D) A non-interswitch toggled form of Arl8-GDP (pdb_id: 1zd9; structural genomics consortium). (E) An interswitch toggled form of Arl8-GDP (pdb_id: 2 h18; structural genomics consortium).