Primary Citation PubMed: 23827680
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Published in 2014
(E) Overlay of the active-site structure of the O6MeG·T–Mn 2+ ternary complex (shown in blue) with that of published G·A–Mn 2+ ternary complex 55 (PDB ID 4LVS, shown in... yellow green, RMSD = 0.655 Å).
Whereas the O6MeG·T–Mn 2+ ternary complex and recently published G·A–Mn 2+ ternary complex 55 are found to be similar in overall structure (PDB ID 4LVS, RMSD = 0.655 Å), the active-site conformations of protein and DNA in both complexes are quite different (Figure 6 E and Figure S3 in SI ).
34 , 49 The B-factors analysis of the active sites of published polβ ternary structures shows that the nascent and the primer terminus base pairs of ternary complex with a matched base pair (e.g., A·U (PDB ID 2FMS, 2.0 Å resolution), 41a A·T (3LK9, 2.5 Å), 41b G·C (2FMP, 1.7 Å), 41a oxoG·C (1MQ3, 2.8 Å) 34 ) are ordered with an average B-factor range of ∼20–30 Å 2 , while those of ternary complex with a mismatched base pair (e.g., C·A (3C2L, 2.6 Å), 42 G·A (3C2M, 2.2 Å), 42 G·A (4LVS, 2.0 Å) 55 ) are disordered with an average B-factor range of ∼40–60 Å 2 , suggesting that the low mobility of the nascent and the primer terminus base pairs is preferred for the formation of a catalytically optimal conformation.
Publication Year: 2014
Complex Sugar pucker Buckle (NBP) ‡ Shear (NBP) Primer † Incoming dC–dGTP C3′-endo C3′-endo 8.5 −0.17 dC–8oxodGTP C3′-endo C4′-e... o −13.1 0.43 dA–8oxodGTP C3′-endo C3′-endo 0.7 0.03 dG–dATP § C2′-endo C3′-endo 43.2 0.61 dA–8oxodGTP Π C2′-endo C4′-exo −13.9 −0.06 * Parameters extracted with 3DNA † Primer Terminus ‡ N ascent B ase P air § PDB ID 4LVS Π PDB ID 3MBY Extended Data Table 3 Data collection and refinement statistics of pol β insertion opposite cytosine with 8-oxo-dGTP and dGTP.
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