2X7V

Crystal structure of Thermotoga maritima endonuclease IV in the presence of zinc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.146 

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This is version 1.1 of the entry. See complete history

Literature

Structure of the Endonuclease Iv Homologue from Thermotoga Maritima in the Presence of Active-Site Divalent Metal Ions

Tomanicek, S.J.Hughes, R.C.Ng, J.D.Coates, L.

(2010) Acta Crystallogr.,Sect.F 66: 1003

  • DOI: 10.1107/S1744309110028575
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The most frequent lesion in DNA is at apurinic/apyrimidinic (AP) sites resulting from DNA-base losses. These AP-site lesions can stall DNA replication and lead to genome instability if left unrepaired. The AP endonucleases are an important class of e ...

    The most frequent lesion in DNA is at apurinic/apyrimidinic (AP) sites resulting from DNA-base losses. These AP-site lesions can stall DNA replication and lead to genome instability if left unrepaired. The AP endonucleases are an important class of enzymes that are involved in the repair of AP-site intermediates during damage-general DNA base-excision repair pathways. These enzymes hydrolytically cleave the 5'-phosphodiester bond at an AP site to generate a free 3'-hydroxyl group and a 5'-terminal sugar phosphate using their AP nuclease activity. Specifically, Thermotoga maritima endonuclease IV is a member of the second conserved AP endonuclease family that includes Escherichia coli endonuclease IV, which is the archetype of the AP endonuclease superfamily. In order to more fully characterize the AP endonuclease family of enzymes, two X-ray crystal structures of the T. maritima endonuclease IV homologue were determined in the presence of divalent metal ions bound in the active-site region. These structures of the T. maritima endonuclease IV homologue further revealed the use of the TIM-barrel fold and the trinuclear metal binding site as important highly conserved structural elements that are involved in DNA-binding and AP-site repair processes in the AP endonuclease superfamily.


    Organizational Affiliation

    Oak Ridge National Laboratory, Neutron Scattering Science Division, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROBABLE ENDONUCLEASE 4
A
287Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
Gene Names: nfo
EC: 3.1.21.2
Find proteins for Q9WYJ7 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9WYJ7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.146 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 123.370α = 90.00
b = 123.370β = 90.00
c = 35.300γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-08
    Type: Initial release
  • Version 1.1: 2012-04-18
    Type: Database references, Derived calculations, Refinement description, Version format compliance