4B9T

Structure of the high fidelity DNA polymerase I with an oxidative formamidopyrimidine-dG DNA lesion -dC basepair in the post-insertion site.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Unexpected Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA Lesions.

Gehrke, T.H.Lischke, U.Gasteiger, K.L.Schneider, S.Arnold, S.Muller, H.C.Stephenson, D.S.Zipse, H.Carell, T.

(2013) Nat Chem Biol 9: 455

  • DOI: https://doi.org/10.1038/nchembio.1254
  • Primary Citation of Related Structures:  
    4B9L, 4B9M, 4B9N, 4B9S, 4B9T, 4B9U, 4B9V

  • PubMed Abstract: 

    8-Oxopurines (8-oxodG and 8-oxodA) and formamidopyrimidines (FaPydG and FaPydA) are major oxidative DNA lesions involved in cancer development and aging. Their mutagenicity is believed to result from a conformational shift of the N9-C1' glycosidic bonds from anti to syn, which allows the lesions to form noncanonical Hoogsteen-type base pairs with incoming triphosphates during DNA replication. Here we present biochemical data and what are to our knowledge the first crystal structures of carbocyclic FaPydA and FaPydG containing DNA in complex with a high-fidelity polymerase. Crystallographic snapshots show that the cFaPy lesions keep the anti geometry of the glycosidic bond during error-free and error-prone replication. The observed dG·dC→dT·dA transversion mutations are the result of base shifting and tautomerization.


  • Organizational Affiliation

    Center for Integrated Protein Science at the Department of Chemistry, Ludwig Maximilians University, Munich, Germany.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA POLYMERASE619Geobacillus stearothermophilusMutation(s): 0 
EC: 2.7.7.7
UniProt
Find proteins for E1C9K5 (Geobacillus stearothermophilus)
Explore E1C9K5 
Go to UniProtKB:  E1C9K5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1C9K5
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*AP*CP*CP*TP*GP*AP*CP*TP*CP*TP)-3'11Geobacillus stearothermophilus
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*CP*AP*TP*FOXP*AP*GP*AP*GP*TP*CP*AP*GP*GP*TP*TP)-3'15Geobacillus stearothermophilus
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.381α = 90
b = 93.775β = 90
c = 105.608γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references, Structure summary
  • Version 1.2: 2013-05-29
    Changes: Database references
  • Version 1.3: 2013-07-03
    Changes: Database references
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description