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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 

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
  • Structures With Same Primary Citation

  • 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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Endonuclease IIIA226Geobacillus stearothermophilusMutation(s): 0 
Gene Names: nth
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*AP*GP*AP*CP*GP*TP*GP*GP*AP*C)-3'B11N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*T*GP*TP*CP*CP*AP*(PED)P*GP*TP*CP*T)-3'C11N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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

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C
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
NA
Query on NA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.826α = 90
b = 106.828β = 90
c = 41.708γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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