Figure 4.

(A) Overlays of the structures of WT Ec Hfq and distal (Y25W), lateral (F11W), proximal edge (F39W) and proximal pore (F42W) Hfq tryptophan mutants. All proteins are shown as cartoons with WT Hfq coloured cyan, Y25W coloured green, F11W coloured red, F39W coloured yellow and F42W coloured blue. The calculated RMSD (listed within the grey box) reveals that each mutation does not affect the protomeric structures significantly. (B) Two close up views of the overlay of the structures of the WT Ec Hfq bound to A₁₅ (blue carbon sticks) and the (Y25W) distal face mutation (green carbon sticks) near the position of the substitution and R-site. Y25W takes two conformations, one of which occurs in 2 out of 6 protomers (left). This conformation would block adenine insertion into the R-site (red box). The second conformation (right) occurs in 5 out of 6 protomers and allows base stacking with adenine. However the 2′ oxygen of the ribose clashes with the indole ring (red arc), requiring adjustment of either the phosphodiester or polypeptide backbone or both to relieve the clash. These two structural problems are likely the cause for the significant reduction in A₁₅ binding to this distal face mutant. (C) Close up of the area about the β2 and β5 strands after overlaying WT Ec Hfq and the F11W hexamers. The two major conformational differences between the F11W protein and WT Hfq are enclosed within the red boxes with position 11 shown and numbered in the rightmost figure.