8VFJ
Polymerase Beta Host Guest Complex Containing FapydG base paired with TMP
Summary for 8VFJ
Entry DOI | 10.2210/pdb8vfj/pdb |
Descriptor | DNA 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 Keywords | fapydg, polymerase beta, host guest, 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 | 47809.87 |
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 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 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: 38634780DOI: 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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