Figure 7.

Model for processivity factor. This figure shows the potential function of vvUDG as a sliding clamp as part of the viral processivity factor and compares the model with the sliding clamp from S. solfataricus. (A) A model of the proposed sliding clamp. Shown is a homotetrameric arrangement of two dimers as observed in both crystal structures of vvUDG. The diameter of the central channel is 27 Å. N-terminal residues 1–16 and C-terminal residues 208–218 that are part of the first dimer interface (see Fig. 2B) and implicated in potential binding to A20 are shown and highlighted (purple). The straight line passing through the central channel indicates a DNA molecule. The possible binding site for A20 is shown. (B) Model of proposed sliding clamp shown as molecular surface colored by electrostatic potential (color code: red electronegative; blue electropositive; white neutral). The view is the same as in Fig. 7A. The electrostatic potential for the highlighted residues in Fig. 7A indicates neutral regions in these locations. (C) Sliding clamp in S. solfataricus (2IX2) [25]. The heterotrimeric sliding clamp PCNA in S. solfataricus is shown as ribbon model (color code: by chain). The diameter of the central channel is 29 Å.