2XGP | pdb_00002xgp

Yeast DNA polymerase eta in complex with C8-2-acetylaminofluorene containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.272 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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 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.

Macromolecule Content 

  • Total Structure Weight: 134.36 kDa 
  • Atom Count: 9,069 
  • Modeled Residue Count: 1,062 
  • Deposited Residue Count: 1,112 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
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
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*CP*8FG*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:  0.272 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.44α = 90
b = 103.44β = 90
c = 292.35γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata 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 2.0: 2017-12-06
    Changes: Advisory, Atomic model, Source and taxonomy
  • Version 2.1: 2023-12-20
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description