1XQP

Crystal structure of 8-oxoguanosine complexed Pa-AGOG, 8-oxoguanine DNA glycosylase from Pyrobaculum aerophilum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

A DNA glycosylase from Pyrobaculum aerophilum with an 8-oxoguanine binding mode and a noncanonical helix-hairpin-helix structure

Lingaraju, G.M.Sartori, A.A.Kostrewa, D.Prota, A.E.Jiricny, J.Winkler, F.K.

(2005) Structure 13: 87-98

  • DOI: 10.1016/j.str.2004.10.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Studies of DNA base excision repair (BER) pathways in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum identified an 8-oxoguanine-DNA glycosylase, Pa-AGOG (archaeal GO glycosylase), with distinct functional characteristics. Here, we describe ...

    Studies of DNA base excision repair (BER) pathways in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum identified an 8-oxoguanine-DNA glycosylase, Pa-AGOG (archaeal GO glycosylase), with distinct functional characteristics. Here, we describe its crystal structure and that of its complex with 8-oxoguanosine at 1.0 and 1.7 A resolution, respectively. Characteristic structural features are identified that confirm Pa-AGOG to be the founding member of a functional class within the helix-hairpin-helix (HhH) superfamily of DNA repair enzymes. Its hairpin structure differs substantially from that of other proteins containing an HhH motif, and we predict that it interacts with the DNA backbone in a distinct manner. Furthermore, the mode of 8-oxoguanine recognition, which involves several hydrogen-bonding and pi-stacking interactions, is unlike that observed in human OGG1, the prototypic 8-oxoguanine HhH-type DNA glycosylase. Despite these differences, the predicted kinked conformation of bound DNA and the catalytic mechanism are likely to resemble those of human OGG1.


    Related Citations: 
    • A novel highly thermostable 8-oxoguanine DNA glycosylase from Pyrobaculum aerophilum
      Sartori, A.A.,Lingaraju, G.M.,Hunziker, P.,Winkler, F.K.,Jiricny, J.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
8-oxoguanine DNA glycosylase
A
256Pyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827)Mutation(s): 0 
Find proteins for Q8ZVK6 (Pyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827))
Go to UniProtKB:  Q8ZVK6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8HG
Query on 8HG

Download SDF File 
Download CCD File 
A
2'-DEOXY-8-OXOGUANOSINE
C10 H13 N5 O5
HCAJQHYUCKICQH-VPENINKCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 72.220α = 90.00
b = 98.110β = 90.00
c = 36.170γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-16
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-04-16
    Type: Experimental preparation
  • Version 1.4: 2017-10-11
    Type: Refinement description