ECOD: An Evolutionary Classification of Protein Domains
Figure 14
ECOD recognizes novel evolutionary relationships.
A) Duf371 (3cbn) forms an 8-stranded β-barrel from intertwined β-strands of a tandem structural duplication. The N-terminal half (blue shades) includes an overside connection between adjacent β-strands (blue) that follows a conserved His (black spheres). The symmetrically related C-terminal half (red shades) includes a similar overside connection (red) following a less conserved His (gray spheres). B) The Duf371 C-terminal repeat (salmon) is rotated about the Z-axis to superimpose (RMSD 1.3) with the N-terminal repeat (slate). C) The GutA-like PTS system IIA component (2f9h) forms a similar duplicated β-barrel. An invariant His in the C-terminal half likely represent the PTS IIA phosphorylation site. D) The PK β-barrel domain-like fold (1pkla1) displays a similar intertwined topology, but retains only a single overside connection (blue) in the N-terminal half. E) PSI-BLAST alignment of the Duf371 repeats detected with Mefer0473 sequence supports the duplication event, with sequence similarities indicated between N-terminal and C-terminal halves. A structure-based alignment of the 2F9H C-terminus is included below. Structural elements (arrow for strand and cylinder for helix) and conservations (calculated by Al2Co [59]) are indicated above/below the corresponding sequences. Conserved positions are highlighted yellow (mainly hydrophobic) and black (polar). Surface representations of F) PTSIIA in the same orientation as in panel C and G) Duf371 in the rotated orientation of panel B are colored in rainbow according to conservation, from blue (less) to red (more).