1U49 | pdb_00001u49

Adenine-8oxoguanine mismatch at the polymerase active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.247 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1U49

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 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. 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.


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

Macromolecule Content 

  • Total Structure Weight: 74.73 kDa 
  • Atom Count: 5,610 
  • Modeled Residue Count: 602 
  • Deposited Residue Count: 606 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase IC [auth A]580Geobacillus stearothermophilusMutation(s): 0 
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
Sequence Annotations
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Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA primer strandA [auth B]11N/A
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA template strand with 8-oxoguanineB [auth C]15N/A
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
D
2N/A
Glycosylation Resources
GlyTouCan: G05551OP
GlyCosmos: G05551OP

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.247 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.382α = 90
b = 93.397β = 90
c = 106.039γ = 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