1ORN

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 

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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:  
    1ORP, 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 (EndoIII) is a [4Fe-4S] cluster-containing DNA glycosylase with repair activity specific for oxidized pyrimidine lesions in duplex DNA ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Endonuclease IIIC [auth A]226Geobacillus stearothermophilusMutation(s): 0 
Gene Names: nth
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*AP*GP*AP*CP*GP*TP*GP*GP*AP*C)-3'A [auth B]11N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*T*GP*TP*CP*CP*AP*(PED)P*GP*TP*CP*T)-3'B [auth C]11N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      SF4
      Query on SF4

      Download Ideal Coordinates CCD File 
      F [auth A]IRON/SULFUR CLUSTER
      Fe4 S4
      LJBDFODJNLIPKO-VKOJMFJBAC
       Ligand Interaction
      TRS
      Query on TRS

      Download Ideal Coordinates CCD File 
      D [auth C]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
      C4 H12 N O3
      LENZDBCJOHFCAS-UHFFFAOYSA-O
       Ligand Interaction
      NA
      Query on NA

      Download Ideal Coordinates CCD File 
      E [auth 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  (Full details and data files)

      • 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