Figure 5

Symmetric CP with significant sequence clues. Proteins with symmetric structure may have symmetric CPs [29]. B. subtilis thiaminase I ([PDB:1YAD]) [51] and Variovorax sp. Pal2 phosphonopyruvate hydrolase ([PDB:2DUA]) [52] shown here are symmetric TIM-barrel proteins. Although their structures can be well-aligned both by linear and CP alignments, significant sequence conservation is observed only in the latter. (a) Linear alignment performed by DALI [36]. The upper text demonstrates that the sequence identity calculated from these structurally aligned residues is 10.1%. Ligand-interacting residues in both proteins are highlighted green; four of them are aligned with identical or physiochemically similar amino acids (gray highlighted strips). The lower image is the superimposition of these two structures. Terminal unaligned regions are shown as ribbons to make the spatial closeness of the termini more easily observable. In this linear alignment, the amino termini of the two proteins are close to each other, as are the carboxyl termini. (b) CP relationship detected by CPSARST. After CP, the sequence identity significantly rises to 24.3% and there are nine ligand-interacting residues aligned with identical or similar amino acids. The amino- and carboxy-terminal halves of 1yadA bounded by the putative CP site are colored cyan and blue, respectively. The orientation of 1yadA in the superimposed image is the same as that in (a). In this CP alignment, the amino and carboxyl termini of the two proteins are separated, a feature of symmetric CP.