Figure 1.

Structure of the Asp-box and short-Asp-box motifs. A. The main chain of the Asp-box of blade 1 of 2bf6 and side chains in highly conserved positions are shown as sticks. The structurally conserved water molecule is shown as a sphere. Coloration is by atom type. Hydrogen bonds involving the four shown side chains and the water molecule are represented by dotted black lines. B. Multiple structural alignment of fifteen Asp-boxes and four s-Asp-boxes. The sequences are labeled with protein name, pdb code, blade number (b) when extracted from β-propellers and propeller number (p) when extracted from a tandem β-propeller. The conserved S, D, G and W are shown in light blue. The vertical green and orange bars mark regular Asp-boxes and s-Asp-boxes respectively. C. Structural overlay of the Asp-boxes in (B). The main chain traces are shown as green ribbons, conserved side chains as sticks colored by atom type, and the conserved water molecules are shown as spheres. D. Same as in (C) but the short Asp-boxes are included. All Asp-boxes are uniformly green and the short-Asp-boxes are colored magenta, yellow, blue and red in order of appearance in the alignment in (B). E. Ramachandran plot for the residues SXDXGXXW of the Asp-box. The blue trace shows average values for phi and psi calculated for the 15 asp-boxes listed in (B). The positions of the conserved residues are indicated by their one letter abbreviation. The trace of standard type I' (red) and type VIII (blue) turns are shown for reference. F. Ramachandran plot for residues SXDXXXW of the s-asp-box. The orange trace shows average values of phi and psi calculated for the 4 s-asp-boxes listed in (B).

Quistgaard and Thirup BMC Structural Biology 2009 9:46   doi:10.1186/1472-6807-9-46
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