Figure 5.

3′ → 5′ exonuclease active site. (A) Stereoribbon representation with modeled DNA using the color code of Fig. 4A (ball-and-stick) and Fig. 2 (ribbons). Active-site residues are shown as ball-and-stick representation. The single-stranded DNA has been taken from the coordinates of RB69–single-stranded DNA complex (21). The orientation of the DNA has been obtained by superimposing the DIE143 motif in Tgo pol with corresponding motif of RB69 gp43 (DIE116). Strand 27 and its preceding loop from the thumb (green) is apparently in collision with the modeled DNA. (B) Comparison of the exonuclease–thumb interface between Tgo pol (color code of Fig. 2B) and RB69 gp43 (gray). In Tgo pol, the lid of the editing site (red) is bent outward compared with the equivalent loop of gp43 (yellow), allowing the tip of the thumb to move several Å (⤡) closer to the exonuclease. This conformation is incompatible with formation of an editing complex [the p(dT)₄ of gp43 is shown as brown space-filling model].