Fig. 5: Crystal structures of post-catalytic Prim–PolC–DNA complexes.

a Schematic of the 1-nt gapped post-turnover DNA substrate found in this pre-ternary post-catalytic complex (top panel). A ribbon-diagram representation of the post-catalytic Prim–PolC–DNA–NTP complex (bottom panel). The catalytic core is coloured sky blue, with the conserved loop structures from this family coloured dark blue, cyan and pink for Loops 1–3, respectively. The catalytic aspartate side chains are represented with the carboxylic oxygens shown in red, and bound manganese ions depicted as magenta spheres. Side chains involved in forming the 5′ phosphate-binding pocket are depicted in dark blue. Active- site geometries of the two forms of post-catalytic turnover Prim–PolC:DNA complex. b In this post-catalytic complex, nucleotidyl transfer has occurred, and inorganic phosphate (PPi) remains bound in the active site. The gate residue, R179, is in the closed conformation, preventing PPi from leaving. All the hydrogen bonds are depicted in black hatched lines, and dative bonding in red hatched lines. Catalytic manganese ions depicted as magenta spheres. c In this post-catalytic complex, PPi has left the active site, and R179 remains in the open conformation, allowing the binding of the next incoming 3′-dUTP in readiness for the next round of catalysis. Regions or side chains that have poor density are represented as transparent elements.