Arf, Arl, Arp and Sar proteins: a family of GTP-binding proteins with a structural device for 'front-back' communication

Abstract

Arf proteins are important regulators of cellular traffic and the founding members of an expanding family of homologous proteins and genomic sequences. They depart from other small GTP-binding proteins by a unique structural device, which we call the 'interswitch toggle', that implements front-back communication from the N-terminus to the nucleotide binding site. Here we define the sequence and structural determinants that propagate information across the protein and identify them in all of the Arf family proteins other than Arl6 and Arl4/Arl7. The positions of these determinants lead us to propose that Arf family members with the interswitch toggle device are activated by a bipartite mechanism acting on opposite sides of the protein. The presence of this communication device might provide a more useful basis for unifying Arf homologs as a family than do the cellular functions of these proteins, which are mostly unrelated. We review available genomic sequences and functional data from this perspective, and identify a novel subfamily that we call Arl8.

Figure 1

The interswitch toggle of human Arf6. Arf6-GDP (Menetrey et al., 2000) (left) and Arf6-GTPγS (Pasqualato et al., 2001) (right) are shown in the same orientation. Residues with disordered electron density are indicated by a dashed line and are expected to interact with membranes in activated Arf. Invariant residues of the signature are shown [drawn with Molscript (Esnouf, 1997)].

Figure 2

The determinants of the interswitch toggle. (A) The hydrogen bond network of the interswitch toggle signature in Arf6-GTPγS. (B) The short interswitch is required for complete retraction of the interswitch. Comparison of the short interswitch of Arf6 to the long interswitch of Ran (Protein Data Bank entries 1A2K and 1K5D). Only the core of Arf6-GTPγS is shown for clarity. (C) The N-terminal hasp fastens the retracted conformation of the interswitch (red) in the GDP-bound structures of human Arf1(Amor et al., 1994) and Arf6 (Menetrey et al., 2000), yeast Arl1(Amor et al., 2001), murine Arl3 (Hillig et al., 2000) and hamster Sar1 (Huang et al., 2001). The spatial volume occupied by the N-terminus is similar in all structures regardless of its exact conformation. Only the core of Arf6-GDP is shown for clarity.

Figure 3

Sequence alignement of human Arf and Arf family proteins. Ran is included to stress the short interswitch of Arf family proteins. Subfamily-distinguishing features detailed in Table I are highlighted in green, interswitch toggle determinants in red. Accession numbers are provided in Supplementary table 3. Alignments were performed with Clustal_W (http://npsa-pbil.ibcp.fr/) and shaded with Boxshade (http://www.ch.embnet.org/software/BOX_form.html). Interspecies alignments are provided in Supplementary figure 4.