1U49

Adenine-8oxoguanine mismatch at the polymerase active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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:  

  • 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
    • 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
    • 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.USA 100: 3895


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase I
A
580Geobacillus stearothermophilusMutation(s): 0 
Gene Names: polA (pol)
EC: 2.7.7.7
Find proteins for P52026 (Geobacillus stearothermophilus)
Go to UniProtKB:  P52026
Entity ID: 1
MoleculeChainsLengthOrganism
DNA primer strandB11N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA template strand with 8-oxoguanineC15N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

Download SDF File 
Download CCD File 
A
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
SO4
Query on SO4

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

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
8OG
Query on 8OG
C
DNA LINKINGC10 H14 N5 O8 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 87.382α = 90.00
b = 93.397β = 90.00
c = 106.039γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
CNSphasing
HKL-2000data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance