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8VFJ

Polymerase Beta Host Guest Complex Containing FapydG base paired with TMP

Summary for 8VFJ
Entry DOI10.2210/pdb8vfj/pdb
DescriptorDNA polymerase beta, DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*(FAP)P*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*TP*AP*TP*GP*CP*GP*C)-3'), ... (6 entities in total)
Functional Keywordsfapydg, polymerase beta, host guest, pol beta, dna binding protein-dna complex, dna binding protein/dna
Biological sourceHomo sapiens (human)
More
Total number of polymer chains4
Total formula weight47809.87
Authors
Oden, P.N.,Ryan, B.J.,Freudenthal, B.D. (deposition date: 2023-12-21, release date: 2024-05-08, Last modification date: 2024-06-05)
Primary citationGao, 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
Cited by
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
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2.14 Å)
Structure validation

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PDB entries from 2024-10-30

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