Fig. 6: Synthesis-dependent template displacement (STD) influences DNA conformation through direct interactions between the gap and a hydrophobic wedge.
From: Molecular basis for DNA repair synthesis on short gaps by mycobacterial Primase-Polymerase C
a A schematic representation of the Prim–PolC/DNA/UTP ternary model emphasising how the splaying of the template strand and bases in the gap is influenced by a hydrophobic wedge (I73/Y74). Surface loops (1–3) also play key roles in orientating the upstream side of the gapped DNA. Loops 1–3 are represented as translucent surfaces coloured blue, salmon and cyan, respectively. The base pairing of the upstream DNA is disrupted at G/C-2 by interactions with Loop 3. The surface of I73/Y74 wedge is coloured yellow. The inset view (below) shows the side-chain interactions that participate in the splaying of the gap bases (A0 and A + 1) of the template strand. b A similar schematic representation of the post-turnover complex with PPi bound in the active site. This structure shows a significant difference in the bending angle and orientation of the upstream DNA following synthesis brought about by the change in splaying angle around the wedge and loss of contacts with Loops 2 and 3, induced by synthesis-dependent template displacement. The surface of I73/Y74 wedge is coloured yellow. The inset view (below) shows the relocation of the second gap base (A + 1) across the wedge into the active site following ribonucleotide incorporation opposite A0. Side chains with poor density are represented as transparent elements.
