Fig. 2: Structure of human PrimPol inserting incorrect dATP opposite the oxoG template base.

a The overall structure of the ternary PrimPol oxoG•dATP complex with the 2′,3′-dideoxy 3′-terminated primer (molecule A of the 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, and the water molecule coordinated by the Ca²⁺ ion is shown as a small red sphere. The oxoG residue (orange) is forming a nascent base pair with the incoming dATP (purple). 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 dATP in the PrimPol active site of the 2′-deoxy-3′-terminated primer (intact 3′-OH group)-containing complex (molecule B of the AU). There are two Ca²⁺ ions (metals ‘A’ and ‘B’) in this complex. The key catalytic residues (Asp114, Glu116, and Asp280), the residues contacting the incoming dCTP (Lys165, Ser167, His169, Arg288, Asn289, Phe290, Arg291, and Lys297), the template oxoG 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. The side chains of Gly74 and Gln75 are disordered in this complex and, thus, not shown. c A simulated annealing Fo−Fc omit map (contoured at 2.5σ-level at 2.40 Å resolution and colored in blue) showing the clear electron density for the entire oxoG residue in the syn conformation, its partner incoming dATP and the Ca²⁺ ‘metal B’ ion observed in the complex with the 2′,3′-dideoxy 3′-terminated primer. Hydrogen bonds are indicated by black dashes. Such oxoG(syn)•dATP base pair arrangement is observed in all mentioned PrimPol oxoG•dATP complexes. d Similar phosphate backbone conformations of C2-oxoG3(syn)-C4 (gray and orange) and unmodified C2-T3-C4 (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.