1ORP

Structure of a Trapped Endonuclease III-DNA Covalent Intermediate: Estranged-Adenine Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a Trapped Endonuclease III-DNA Covalent Intermediate

Fromme, J.C.Verdine, G.L.

(2003) Embo J. 22: 3461-3471

  • DOI: 10.1093/emboj/cdg311
  • Primary Citation of Related Structures:  1ORN, 1P59

  • PubMed Abstract: 
  • Nearly all cells express proteins that confer resistance to the mutagenic effects of oxidative DNA damage. The primary defense against the toxicity of oxidative nucleobase lesions in DNA is the base-excision repair (BER) pathway. Endonuclease III (En ...

    Nearly all cells express proteins that confer resistance to the mutagenic effects of oxidative DNA damage. The primary defense against the toxicity of oxidative nucleobase lesions in DNA is the base-excision repair (BER) pathway. Endonuclease III (EndoIII) is a [4Fe-4S] cluster-containing DNA glycosylase with repair activity specific for oxidized pyrimidine lesions in duplex DNA. We have determined the crystal structure of a trapped intermediate that represents EndoIII frozen in the act of repairing DNA. The structure of the protein-DNA complex provides insight into the ability of EndoIII to recognize and repair a diverse array of oxidatively damaged bases. This structure also suggests a rationale for the frequent occurrence in certain human cancers of a specific mutation in the related DNA repair protein MYH.


    Organizational Affiliation

    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Endonuclease III
A
226N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*AP*GP*AP*CP*AP*TP*GP*GP*AP*C)-3'B11N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*TP*CP*CP*AP*(PED)P*GP*TP*CP*T)-3'C11N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PED
Query on PED
C
NON-POLYMERC5 H13 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.241 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 67.732α = 90.00
b = 106.516β = 90.00
c = 41.661γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-15
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance