Fig. 3: Structure of human PrimPol extending from a correct primer C base opposite the oxoG template base.

a The overall structure of the ternary PrimPol oxoG•C extension complex (molecule A of the asymmetric unit, AU). The N-helix and modules ModN and ModC are shown in cartoon representation in dark blue, yellow, and cyan, respectively. The DNA is shown as gray sticks, the Ca²⁺ ion (‘metal B’) is shown as a light blue sphere. The oxoG residue (orange) is forming a base pair with the primer terminal C base (red). The incoming dATP forms a nascent base pair with a template T base, which is 5′-adjacent to the oxoG residue. The unstructured regions in the ModN and ModC modules are shown as dashed yellow and cyan lines, respectively. The side chains of key catalytic active-site residues Asp114, Glu116, and Asp280 are shown as red sticks. b A close-up view of the oxoG template base and the 3′-deoxy primer C14 base in the PrimPol active site (molecule B in the AU). There are two Ca²⁺ ions (metal ‘A’ and ‘B’) in this complex shown as light blue spheres, and the water molecule coordinated by the Ca²⁺ ion is shown as a small red sphere. The key catalytic residues (Asp114, Glu116, and Asp280), the residues contacting the incoming dATP (Lys165, Ser167, His169, Arg288, Asn289, Phe290, Arg291, and Lys297), the templating base (Gly74, Gln75, and Arg76), and the rest of the template strand (Lys10, His46, and Arg47) are shown in sticks and with oxygen atoms in bright red and nitrogen atoms in blue. c A simulated annealing Fo−Fc omit map (contoured at 2.5σ-level at 2.10 Å resolution and colored in blue) showing the clear electron density for the entire oxoG residue in the anti conformation and its partner C14 residue. Hydrogen bonds are indicated by black dashes. d Similar phosphate backbone conformations of T3-oxoG4(anti)-C5 (gray and orange) and unmodified T3-C4-G5 (beige) template strand segments within the PrimPol active site of their respective ternary complexes. The complexes are superimposed by ModN and ModC of PrimPol protein. The main-chain nitrogen atom of Gln48 contacts the oxygen atom of the phosphate group of the oxoG(anti), similarly to its contact with the phosphate group of the C4 in the unmodified complex. The guanidinium group of Arg47 of ModN, however, repositions to contact a neighboring protein chain in the crystal (main-chain oxygen atom of Gly124 of a symmetry-related molecule, not shown).