Supplementary Figure 5: Structural changes in T5Fen after DNA binding.
From: Direct observation of DNA threading in flap endonuclease complexes
(a) Schematic showing differences between DNA-bound (complex TC2, magenta) and substrate-free T5Fen structures (green). Residues connecting helices 1 to 2 and 9 to 10 and in helix 4 undergo the largest changes. Helices numbered in white. The junction of helices 4 and 5 is shifted ~ 5-7 Å toward the H3TH motif (h9 and h10) upon binding DNA as shown by the double headed arrow (right panel). (b) Rearrangement of residues 84–92 upon DNA binding. Yellow dashes (with distances) show the largest movements. Atoms of residues labeled in black undergo minimal (<2 Å) translations. Colored labels indicate movement of >2 Å. (c) Two views showing the range of movement observed for helix 4 residues and Arg86 (sticks) in DNA-free, looped-out conformer (cyan cartoon), and with intact substrate bound in complex C2 (magenta cartoon), and in pseudo-product complex C3 (yellow cartoon). The numbered orange spheres show the position of three metal ions (1 and 2 in Cat1 and ion 3 in Cat2. (d) Residues on the helix 1 (h1) and the loop to helix 2 (h2) undergo the next largest rearrangements with His36 playing a role in DNA binding. In one DNA-free form this loop is disordered (not shown). (e) Two views of the H3TH motif (helices h9 and h10) showing residues moving >2 Å upon DNA binding. L202 which changes conformation upon engaging substrate and conserved residues shown in stick representation.
