3OHB

Yeast DNA polymerase eta extending from an 8-oxoG lesion

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 


Literature

Structural basis for error-free replication of oxidatively damaged DNA by yeast DNA polymerase eta.

Silverstein, T.D., Jain, R., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

(2010) Structure 18: 1463-1470

  • DOI: https://doi.org/10.1016/j.str.2010.08.019
  • Primary Citation of Related Structures:  
    3OHA, 3OHB

  • PubMed Abstract: 

    7,8-dihydro-8-oxoguanine (8-oxoG) adducts are formed frequently by the attack of oxygen-free radicals on DNA. They are among the most mutagenic lesions in cells because of their dual coding potential, where, in addition to normal base-pairing of 8-oxoG(anti) with dCTP, 8-oxoG in the syn conformation can base pair with dATP, causing G to T transversions. We provide here for the first time a structural basis for the error-free replication of 8-oxoG lesions by yeast DNA polymerase η (Polη). We show that the open active site cleft of Polη can accommodate an 8-oxoG lesion in the anti conformation with only minimal changes to the polymerase and the bound DNA: at both the insertion and post-insertion steps of lesion bypass. Importantly, the active site geometry remains the same as in the undamaged complex and provides a basis for the ability of Polη to prevent the mutagenic replication of 8-oxoG lesions in cells.

    • Organizational Affiliation: 

    Department of Structural & Chemical Biology, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, NY 10029, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase eta520Saccharomyces cerevisiaeMutation(s): 2 
Gene Names: DBH1, RAD30, YDR419W
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(*TP*AP*AP*TP*GP*(8OG)P*AP*GP*GP*GP*GP*AP*GP*GP*AP*C)-3'B [auth T]16N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*GP*TP*CP*CP*TP*CP*CP*CP*CP*TP*(DOC))-3'C [auth P]11N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.958α = 90
b = 228.268β = 90
c = 85.932γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description