FIGURE 1.

3D model of Rpp1p shows structural similarity to Ph1877p (PDB code 1V77). (A) The initial alignment of Rpp1p and YcdX was obtained from the 3D-Jury meta-server (Ginalski et al. 2003). Slight manual adjustments were made to position insertions and deletions within loop regions. The residues are color-coded according to the following scheme: (red letters) negative residues; (green shade) aliphatic; (blue letters) positive; (light-blue letters) aromatic; (orange letters) charged; (purple) small; (red shade) polar; (cyan shade) big; (dark-blue shade) hydrophobic. Red triangles beneath the alignment denote conserved acidic residues of Rpp1p and are equivalent to red triangles in Supplemental Figure 1 (see text for details). (B) The model of Rpp1p was colored by sequence conservation so that most conserved residues are in red and the least conserved ones are in blue (Pei and Grishin 2001). The color palette between red and blue indicates intermediate levels of sequence conservation. The positions of ions in the putative trinuclear metal cluster (blue spheres inside the β-barrel) have been assigned from the template structure (Teplyakov et al. 2003). (C) The Ph1877p structure (Takagi et al. 2004) was aligned to the Rpp1p model using CE (Shindyalov and Bourne 1998). The optimal alignment spans 192 residues with an overall RMSD of 3.57 Å. Helices are colored differently from β-strands and loops to facilitate the comparison of secondary structure elements with Figure 1B.