3FHF

Crystal structure of Methanocaldococcus jannaschii 8-oxoguanine DNA glycosylase (MjOgg)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.995 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of two archaeal 8-oxoguanine DNA glycosylases provide structural insight into guanine/8-oxoguanine distinction.

Faucher, F.Duclos, S.Bandaru, V.Wallace, S.S.Doublie, S.

(2009) Structure 17: 703-712

  • DOI: 10.1016/j.str.2009.03.007
  • Primary Citation of Related Structures:  3FHG

  • PubMed Abstract: 
  • Among the four DNA bases, guanine is particularly vulnerable to oxidative damage and the most common oxidative product, 7,8-dihydro-8-oxoguanine (8-oxoG), is the most prevalent lesion observed in DNA molecules. Fortunately, 8-oxoG is recognized and e ...

    Among the four DNA bases, guanine is particularly vulnerable to oxidative damage and the most common oxidative product, 7,8-dihydro-8-oxoguanine (8-oxoG), is the most prevalent lesion observed in DNA molecules. Fortunately, 8-oxoG is recognized and excised by the 8-oxoguanine DNA glycosylase (Ogg) of the base excision repair pathway. Ogg enzymes are divided into three separate families, namely, Ogg1, Ogg2, and archaeal GO glycosylase (AGOG). To date, structures of members of both Ogg1 and AGOG families are known but no structural information is available for members of Ogg2. Here we describe the first crystal structures of two archaeal Ogg2: Methanocaldococcus janischii Ogg and Sulfolobus solfataricus Ogg. A structural comparison with OGG1 and AGOG suggested that the C-terminal lysine of Ogg2 may play a key role in discriminating between guanine and 8-oxoG. This prediction was substantiated by measuring the glycosylase/lyase activity of a C-terminal deletion mutant of MjaOgg.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-glycosylase/DNA lyase
A
214Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Gene Names: ogg
EC: 3.2.2.-, 4.2.99.18
Find proteins for Q58134 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q58134
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.995 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 89.440α = 90.00
b = 37.840β = 116.08
c = 75.010γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CNSrefinement
SHARPphasing
Blu-Icedata collection
SCALAdata scaling
XDSdata reduction
SCALAdata processing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-03-21
    Type: Database references