3I0W

Crystal structure of Clostridium acetobutylicum 8-oxoguanine glycosylase/lyase in complex with dsDNA containing cytosine opposite to 8-oxoG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the lack of opposite base specificity of Clostridium acetobutylicum 8-oxoguanine DNA glycosylase.

Faucher, F.Wallace, S.S.Doublie, S.

(2009) DNA Repair (Amst) 8: 1283-1289

  • DOI: 10.1016/j.dnarep.2009.08.002
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • 7,8-Dihydro-8-oxoguanine (8-oxoG) is the major oxidative product of guanine and the most prevalent base lesion observed in DNA molecules. Because 8-oxoG has the capability to form a Hoogsteen pair with adenine (8-oxoG:A) in addition to a normal Watso ...

    7,8-Dihydro-8-oxoguanine (8-oxoG) is the major oxidative product of guanine and the most prevalent base lesion observed in DNA molecules. Because 8-oxoG has the capability to form a Hoogsteen pair with adenine (8-oxoG:A) in addition to a normal Watson-Crick pair with cytosine (8-oxoG:C), this lesion can lead to a G:C-->T:A transversion after replication. However, 8-oxoG is recognized and excised by the 8-oxoguanine DNA glycosylase (Ogg) of the base excision repair pathway. Members of the Ogg1 family usually display a strong preference for a C opposite the lesion. In contrast, the atypical Ogg1 from Clostridium actetobutylicum (CacOgg) can excise 8-oxoG when paired with either one of the four bases, albeit with a preference for C and A. Here we describe the first high-resolution crystal structures of CacOgg in complex with duplex DNA containing the 8-oxoG lesion paired to cytosine and to adenine. A structural comparison with human OGG1 provides a rationale for the lack of opposite base specificity displayed by the bacterial Ogg.


    Organizational Affiliation

    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405-0068, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
8-oxoguanine-DNA-glycosylaseA290Clostridium acetobutylicumMutation(s): 1 
Gene Names: CAC2707CA_C2707
EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
Find proteins for Q97FM4 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787))
Explore Q97FM4 
Go to UniProtKB:  Q97FM4
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3'B13N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*A)-3'C12N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.4α = 90
b = 92.4β = 90
c = 191.05γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance