1U4B

Extension of an adenine-8oxoguanine mismatch


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 

wwPDB Validation 3D Report Full Report



Literature

Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase.

Hsu, G.W.Ober, M.Carell, T.Beese, L.S.

(2004) Nature 431: 217-221

  • DOI: 10.1038/nature02908
  • Primary Citation of Related Structures:  
    1U4B, 1U47, 1U45, 1U49, 1U48

  • PubMed Abstract: 
  • Aerobic respiration generates reactive oxygen species that can damage guanine residues and lead to the production of 8-oxoguanine (8oxoG), the major mutagenic oxidative lesion in the genome. Oxidative damage is implicated in ageing and cancer, and it ...

    Aerobic respiration generates reactive oxygen species that can damage guanine residues and lead to the production of 8-oxoguanine (8oxoG), the major mutagenic oxidative lesion in the genome. Oxidative damage is implicated in ageing and cancer, and its prevalence presents a constant challenge to DNA polymerases that ensure accurate transmission of genomic information. When these polymerases encounter 8oxoG, they frequently catalyse misincorporation of adenine in preference to accurate incorporation of cytosine. This results in the propagation of G to T transversions, which are commonly observed somatic mutations associated with human cancers. Here, we present sequential snapshots of a high-fidelity DNA polymerase during both accurate and mutagenic replication of 8oxoG. Comparison of these crystal structures reveals that 8oxoG induces an inversion of the mismatch recognition mechanisms that normally proofread DNA, such that the 8oxoG.adenine mismatch mimics a cognate base pair whereas the 8oxoG.cytosine base pair behaves as a mismatch. These studies reveal a fundamental mechanism of error-prone replication and show how 8oxoG, and DNA lesions in general, can form mismatches that evade polymerase error-detection mechanisms, potentially leading to the stable incorporation of lethal mutations.


    Related Citations: 
    • Structures of Mismatch Replication Errors Observed in a DNA Polymerase
      Johnson, S.J., Beese, L.S.
      (2004) Cell 116: 803
    • Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations
      Johnson, S.J., Taylor, J.S., Beese, L.S.
      (2003) Proc Natl Acad Sci U S A 100: 3895
    • Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal
      Kiefer, J.R., Mao, C., Braman, J.C., Beese, L.S.
      (1998) Nature 391: 304

    Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase IA580Geobacillus stearothermophilusMutation(s): 0 
Gene Names: polApol
EC: 2.7.7.7
Find proteins for P52026 (Geobacillus stearothermophilus)
Explore P52026 
Go to UniProtKB:  P52026
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA primer strandB13N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA template strand with 8-oxoguanineC15N/A
      Oligosaccharides

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      Entity ID: 4
      MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
      beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
      D
      2 N/A Oligosaccharides Interaction
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      SO4
      Query on SO4

      Download CCD File 
      A
      SULFATE ION
      O4 S
      QAOWNCQODCNURD-UHFFFAOYSA-L
       Ligand Interaction
      MG
      Query on MG

      Download CCD File 
      A
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Biologically Interesting Molecules (External Reference) 1 Unique
      Entity ID: 4
      IDChainsNameType/Class2D Diagram3D Interactions
      PRD_900003
      Query on PRD_900003
      DsucroseOligosaccharide /  Nutrient

      --

      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.60 Å
      • R-Value Free: 0.227 
      • R-Value Work: 0.213 
      • R-Value Observed: 0.213 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 86.313α = 90
      b = 93.494β = 90
      c = 106.372γ = 90
      Software Package:
      Software NamePurpose
      HKL-2000data collection
      SCALEPACKdata scaling
      CNSrefinement
      HKL-2000data reduction
      CNSphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2004-09-14
        Type: Initial release
      • Version 1.1: 2008-04-30
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 2.0: 2020-07-29
        Type: Remediation
        Reason: Carbohydrate remediation
        Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary