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Results: 7

1.
Figure 3.

Figure 3. From: DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion.

R238K pol β binary complex with a templating 8-oxoG in the active site. (A) Overlay of the wild-type (PDB ID 3ISB) and R283K (PDB ID 4GXI) pol β binary complex structures in grey and purple, respectively. (B) A FoFc omit map (green) contoured at 2.5σ is shown for the templating 8-oxoG in the R283K pol β binary structure. The templating 8-oxoG can be modelled in both the syn- and anti-conformations with the phosphate backbone in two orientations.

Bret D. Freudenthal, et al. Nucleic Acids Res. 2013 February;41(3):1848-1858.
2.
Figure 6.

Figure 6. From: DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion.

R283K pol β ternary complex with a templating anti-8-oxoG and incoming dAMPCPP. The templating anti-8-oxoG, incoming dAMPCPP and α-helix (Helix) N are shown in green. Mn2+ and water molecules are shown as red and blue spheres, respectively. (A) Active site of the R283K pol β anti-8-oxoG:dAMPCPP with a FoFc map (green) contoured at 3σ. (B) Key active site hydrogen bonding interactions between the templating anti-8-oxoG and incoming dATP are shown with black dashes. The key amino acids are shown in stick format and the octahedral geometry for each metal ion is illustrated.

Bret D. Freudenthal, et al. Nucleic Acids Res. 2013 February;41(3):1848-1858.
3.
Figure 1.

Figure 1. From: DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion.

Structural overview of wild-type pol β with templating 8-oxoG in the active site. (A) Overlay of the templating anti-G:dCMPCPP (PDB ID 2FMP), anti-8-oxoG:dCMP(CF2)PP (PDB ID 3RJI) and syn-8-oxoG:dAMPCPP (PDB ID 3RJF) in the pol β active site are shown in yellow, salmon and purple, respectively. The position of the templating phosphate backbone is indicated for each conformation. (B) Structure of the closed ternary pol β complex with a templating syn-8-oxoG Hoogsteen base pairing with dAMPCPP (PDB ID 3RJF) (7). The primer terminus (O3′) is indicated. Key hydrogen bonding interactions are shown as black dashes.

Bret D. Freudenthal, et al. Nucleic Acids Res. 2013 February;41(3):1848-1858.
4.
Figure 4.

Figure 4. From: DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion.

R283K pol β ternary complex with a templating anti-8-oxoG:dCMP(CF2)PP base pair. (A) R283K pol β ternary complex active site with 8-oxoG in the anti-conformation base pairing with dCMP(CF2)PP. The key hydrogen bonding interactions are shown as black dashes. Mn2+ and water molecules are shown as red and blue spheres, respectively. The key active site residues and Lys283 (K283) are shown in stick format. (B) Structural overlay of the wild-type and R283K pol β ternary complexes are shown in salmon and cyan, respectively. Mn2+ from the R283K pol β structure is shown as red spheres and the Mg2+ from the wild-type pol β structure is shown in green.

Bret D. Freudenthal, et al. Nucleic Acids Res. 2013 February;41(3):1848-1858.
5.
Figure 2.

Figure 2. From: DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion.

Steady-state kinetic analysis of wild-type and R283K pol β. (A) A discrimination plot of 1-nt gap filling by wild-type and R283K pol β opposite non-damaged guanine (G) and 8-oxoG (8oG) with dCTP or dATP in the presence of MnCl2. The dCTP and dATP incorporation is shown with a green and red bar, respectively. The black arrow highlights the impact of the R283K mutation on dATP incorporation opposite 8-oxoG. (B) Table of select DNA polymerases (polymerase family) that have been characterized kinetically for incorporation opposite 8-oxoG (6,18,19,20–32). The dCTP/dATP ratio shows the preference for incorporation of dCTP relative to dATP. A value of 1 indicates no preference of incorporation, a value >1 indicates a preference for dCTP and a value <1 indicates a preference for dATP incorporation. The likely preferred glycosidic conformation of the templating 8-oxoG is indicated.

Bret D. Freudenthal, et al. Nucleic Acids Res. 2013 February;41(3):1848-1858.
6.
Figure 5.

Figure 5. From: DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion.

Intermediate conformation of the R283K pol β ternary complex with templating anti-8-oxoG and incoming dAMPCPP. (A) Structural overlay of the R283K anti-8-oxoG:dAMPCPP ternary complex with the wild-type open binary (PDB ID 3ISB) and closed ternary (PDB ID 2FMS) pol β complexes shown in green, purple and yellow, respectively. The lyase domain and α-helix N (Helix N) are indicated. The position of α-helix N is designated as open, intermediate (Int.) or closed for each structure. The incoming nucleotide for the R283K ternary complex is coloured green in the active site. (B) Key amino acids that are repositioned during subdomain closure are shown for the open (PDB ID 3ISB), intermediate (R283K 8-oxoG:dATP) and closed (PDB ID 2FMS) pol β complexes. Helix N is shown in a ribbon representation and key amino acids are in stick format. Mn2+ and Mg2+ are shown as red and yellow spheres, respectively.

Bret D. Freudenthal, et al. Nucleic Acids Res. 2013 February;41(3):1848-1858.
7.
Figure 7.

Figure 7. From: DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion.

Structural comparison of R283K anti-8-oxoG:dAMPCPP and wild-type pol β ternary complexes. Active site aspartate residues (D190, D192 and D256), residue 283 (K283 or R283), templating 8-oxoG, incoming nucleotide and the primer terminus (O3′) are indicated. (A) Structural overlay of the R283K anti-8-oxoG:dAMPCPP and wild-type syn-8-oxoG:dAMPCPP pol β ternary complexes are shown in green and purple, respectively. The key movements of the primer terminus and templating strand are highlighted with red arrows. The templating nucleotide is labelled n and its upstream neighbour is n − 1. (B) Structural overlay of the R283K anti-8-oxoG:dATP and mismatch wild-type G:dATP pol β (PDB ID 3C2M) ternary complexes are shown in green and brown, respectively. (C) Key amino acid contacts between the active site residues and the templating base or incoming nucleotide of the R283K anti-8-oxoG:dATP and mismatch wild-type G:dATP pol β ternary complexes are shown with green and brown dashes, respectively. The movement of the phosphate backbone as a result of the adducted oxygen on 8-oxoG templating base is highlighted with a red arrow.

Bret D. Freudenthal, et al. Nucleic Acids Res. 2013 February;41(3):1848-1858.

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