4B9V

Structure of the high fidelity DNA polymerase I with extending from an oxidative formamidopyrimidine-dG DNA lesion -dA basepair.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 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 ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA POLYMERASEA619Geobacillus stearothermophilusMutation(s): 0 
Gene Names: polA
EC: 2.7.7.7
UniProt
Find proteins for E1C9K5 (Geobacillus stearothermophilus)
Explore E1C9K5 
Go to UniProtKB:  E1C9K5
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*TP*AP*AP)-3'B11Geobacillus stearothermophilus
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*AP*TP*FOXP*AP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3'C15Geobacillus stearothermophilus
      Protein Feature View
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      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.00 Å
      • R-Value Free: 0.215 
      • R-Value Work: 0.187 
      • R-Value Observed: 0.188 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 87.901α = 90
      b = 94.035β = 90
      c = 105.341γ = 90
      Software Package:
      Software NamePurpose
      REFMACrefinement
      XDSdata reduction
      SCALAdata scaling
      PHASERphasing

      Structure Validation

      View Full Validation Report




      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