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


This is version 2.1 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: https://doi.org/10.1038/nature02908
  • Primary Citation of Related Structures:  
    1U45, 1U47, 1U48, 1U49, 1U4B

  • 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 its prevalence presents a constant challenge to DNA polymerases that ensure accurate transmission of genomic information ...

    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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase IC [auth A]580Geobacillus stearothermophilusMutation(s): 0 
Gene Names: polA, pol
EC: 2.7.7.7
UniProt
Find proteins for P52026 (Geobacillus stearothermophilus)
Explore P52026 
Go to UniProtKB:  P52026
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52026
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA primer strandA [auth B]13N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA template strand with 8-oxoguanineB [auth C]15N/A
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
D
2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900003
Query on PRD_900003
D
sucroseOligosaccharide / Nutrient Ligand Interaction
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 2.1: 2023-08-23
    Changes: Data collection, Database references, Refinement description, Structure summary