Phylogenetic analysis of Sec7-domain-containing Arf nucleotide exchangers - PubMed (original) (raw)

Figure 4.

Multiple alignments of the Sec7 domain arranged by group. (A) Visual representation of the multiple alignment strength in the Sec7 catalytic domain. As in Figure 3, except all cross-group homologies, including those with limited quality, are shown as colored areas. In addition, the gray areas indicating regions with no intragroup sequence similarity are embedded in white spaces whose width indicates the maximum insert size. (B) Positions of the HC amino acids identified here (further described in Table 4). (C) Positions of previously characterized mutations that affect Arf GEF activity. The top row indicates the wild-type sequence and the bottom row shows the target mutations. Color from red to green indicates the proportion (from 0 to 100%) of wild-type activity expressed by the mutant. Mutations that abolish Arf binding are indicated by *. CYH1 mutant coordinates: E157K, V179A, Y187A, M195A, D207A, K208A, K208E, R219A, and E157A (Betz et al., 1998). ARNO/CYH2 mutant coordinates: E117K, R152E, E156K, M194A, and N201A (Cherfils et al., 1998). (D) Arf contacts. The positions of the 15 amino acids that make contact with Arf in the cocrystal (Goldberg, 1998). See coordinates in F legend. (E) BFA sensitivity consensus. The positions of the amino acids, which are proposed here to define a consensus for BFA sensitivity (Table 5). See structural positions in G. (F) Arf contact sites. The Arf-binding surface in the hydrophobic groove is shown on the three-dimensional structure of the Sec7 domain of S. cerevisiae GEA2 (by x-ray crystallography). Numbered green solid arrows indicate the 10 predicted alpha helices. Light blue indicates predicted loops. Bright blue sequences correspond to the Arf-contact sites positioned in the hydrophobic grove as defined in the Arf–Sec7 domain complex (Renault et al., 2002). Yellow indicates the catalytic glutamic acid. The N-side of the groove is composed of helices α1–5, the glutamate finger loop, and N-the terminal half of helix α7. The C-terminal side includes helices α6, the C-terminal half of helix α7 and helices α8–10. Positions for amino acids are, in S. cerevisiae Gea2 coordinates: R650, L651, G653, S655, Q656, I658, D696, F699, I700, Y703, I706, M707, D711, and V717. (G) BFA sensitivity consensus. As in F, except that yellow sequences correspond to amino acids that are predicted to define BFA sensitivity shown in E and Table 5. Positions for consensus sites are in S. cerevisiae Gea2 coordinates: Y703, S704, M707, D711, and M721. (H) HC amino acids. HC amino acids are positioned on both sides of the Sec7 domain. Two 180° opposite views of the Sec7 domain are shown: front and back. Red indicates HC sites shown in B and Table 4. Limited overlap, 4/16, exists between HC amino acids and Arf contact sites of the Sec7 domain.