Fig. 1: Crystal structure of a ternary Prim–PolC–DNA–NTP complex.
From: Molecular basis for DNA repair synthesis on short gaps by mycobacterial Primase-Polymerase C
a Schematic of the 2-nt gapped DNA substrate found in the ternary complex (top panel). The bottom panel shows a ribbon-diagram representation of the Prim–PolC–DNA–NTP complex (PDBID: 6SA0). 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. The incoming nucleotide, rUTP (UpNHpp), is coloured green. Side chains involved in forming the 5′ phosphate-binding pocket are depicted in dark blue. b Molecular interactions of the N-terminal region of Prim–PolC with the 5′-phosphate moiety (downstream stand) and the dsDNA/ssDNA junction. c Details of the interactions of Loop 3 with upstream template DNA. The primer strand is removed for clarity. d A view of the solvent-accessible surfaces of Loops 2 (cyan) and 3 (salmon) interacting with the upstream DNA duplex. N321 is shown to interdigitate into the DNA duplex and, with P320, cause the DNA to unpair at the −2 position. Loop 2 supports the primer strand of the upstream duplex.
