8VFF

Binary DNA Polymerase Beta bound to DNA containing primer terminal FapydG base-paired with a dA

Summary for 8VFF

• Entry DOI: 10.2210/pdb8vff/pdb
• Descriptor: DNA polymerase beta, DNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(FAP))-3'), ... (6 entities in total)
• Functional Keywords: fapydg, polymerase beta, primer terminus, pol beta, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 4
• Total formula weight: 47795.89

Authors

Oden, P.N.,Ryan, B.J.,Freudenthal, B.D. (deposition date: 2023-12-21, release date: 2024-05-15, Last modification date: 2024-06-05)

Primary citation

Gao, S.,Oden, P.N.,Ryan, B.J.,Yang, H.,Freudenthal, B.D.,Greenberg, M.M.
Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase beta.
Nucleic Acids Res., 52:5392-5405, 2024

PubMed Abstract: N6-(2-deoxy-α,β-d-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamido-pyrimidine (Fapy•dG) is formed from a common intermediate and in comparable amounts to the well-studied mutagenic DNA lesion 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-OxodGuo). Fapy•dG preferentially gives rise to G → T transversions and G → A transitions. However, the molecular basis by which Fapy•dG is processed by DNA polymerases during this mutagenic process remains poorly understood. To address this we investigated how DNA polymerase β (Pol β), a model mammalian polymerase, bypasses a templating Fapy•dG, inserts Fapy•dGTP, and extends from Fapy•dG at the primer terminus. When Fapy•dG is present in the template, Pol β incorporates TMP less efficiently than either dCMP or dAMP. Kinetic analysis revealed that Fapy•dGTP is a poor substrate but is incorporated ∼3-times more efficiently opposite dA than dC. Extension from Fapy•dG at the 3'-terminus of a nascent primer is inefficient due to the primer terminus being poorly positioned for catalysis. Together these data indicate that mutagenic bypass of Fapy•dG is likely to be the source of the mutagenic effects of the lesion and not Fapy•dGTP. These experiments increase our understanding of the promutagenic effects of Fapy•dG.

PubMed: 38634780
DOI: 10.1093/nar/gkae277

Experimental method

X-RAY DIFFRACTION (1.69 Å)