2XGQ

Structure of yeast DNA polymerase eta in complex with C8-N-acetyl-2- aminoanthracene containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Mechanism of Replication Blocking and Bypass of Y-Family Polymerase Eta by Bulky Acetylaminofluorene DNA Adducts.

Schorr, S.Schneider, S.Lammens, K.Hopfner, K.P.Carell, T.

(2010) Proc Natl Acad Sci U S A 107: 20720

  • DOI: https://doi.org/10.1073/pnas.1008894107
  • Primary Citation of Related Structures:  
    2XGP, 2XGQ

  • PubMed Abstract: 

    Heterocyclic aromatic amines produce bulky C8 guanine lesions in vivo, which interfere and disrupt DNA and RNA synthesis. These lesions are consequently strong replication blocks. In addition bulky adducts give rise to point and frameshift mutations. The translesion synthesis (TLS) DNA polymerase η is able to bypass slowly C8 bulky adduct lesions such as the widely studied 2-aminofluorene-dG and its acetylated analogue mainly in an error-free manner. Replicative polymerases are in contrast fully blocked by the acetylated lesion. Here, we show that TLS efficiency of Pol η depends critically on the size of the bulky adduct forming the lesion. Based on the crystal structure, we show why the bypass reaction is so difficult and we provide a model for the bypass reaction. In our model, TLS is accomplished without rotation of the lesion into the anti conformation as previously thought.


  • Organizational Affiliation

    Department of Chemistry, Center for Integrated Protein Science CIPS, Ludwig-Maximilians University, D-81377 Munich, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA POLYMERASE ETA
A, B
536Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.7
UniProt
Find proteins for Q04049 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04049 
Go to UniProtKB:  Q04049
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04049
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'C [auth P],
D [auth Q]
9N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*CP*8AG*CP*TP*CP*AP*TP*CP*CP*AP*C)-3'E [auth T],
F [auth U]
11N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.525α = 90
b = 103.525β = 90
c = 292.657γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-03
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-08
    Changes: Advisory, Source and taxonomy
  • Version 2.0: 2019-05-15
    Changes: Advisory, Data collection, Derived calculations, Polymer sequence
  • Version 2.1: 2023-12-20
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description