1DE8

HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE-1 (APE1) BOUND TO ABASIC DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination [corrected

Mol, C.D., Izumi, T., Mitra, S., Tainer, J.A.

(2000) Nature 403: 451-456

  • DOI: 10.1038/35000249
  • Primary Citation of Related Structures:  
    1DE9, 1DE8, 1DEW

  • PubMed Abstract: 

    • Non-coding apurinic/apyrimidinic (AP) sites in DNA are continually created in cells both spontaneously and by damage-specific DNA glycosylases. The biologically critical human base excision repair enzyme APE1 cleaves the DNA sugar-phosphate backbone at a ...

    Non-coding apurinic/apyrimidinic (AP) sites in DNA are continually created in cells both spontaneously and by damage-specific DNA glycosylases. The biologically critical human base excision repair enzyme APE1 cleaves the DNA sugar-phosphate backbone at a position 5' of AP sites to prime DNA repair synthesis. Here we report three co-crystal structures of human APE1 bound to abasic DNA which show that APE1 uses a rigid, pre-formed, positively charged surface to kink the DNA helix and engulf the AP-DNA strand. APE1 inserts loops into both the DNA major and minor grooves and binds a flipped-out AP site in a pocket that excludes DNA bases and racemized beta-anomer AP sites. Both the APE1 active-site geometry and a complex with cleaved AP-DNA and Mn2+ support a testable structure-based catalytic mechanism. Alanine substitutions of the residues that penetrate the DNA helix unexpectedly show that human APE1 is structurally optimized to retain the cleaved DNA product. These structural and mutational results show how APE1 probably displaces bound glycosylases and retains the nicked DNA product, suggesting that APE1 acts in vivo to coordinate the orderly transfer of unstable DNA damage intermediates between the excision and synthesis steps of DNA repair.

    Organizational Affiliation: 

    Skaggs Institute for Chemical Biology, and the Department of Molecular Biology, La Jolla, California 92037-1027, USA.



Macromolecules

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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MAJOR APURINIC/APYRIMIDINIC ENDONUCLEASE A, B276Homo sapiensMutation(s): 0 
Gene Names: APEX1, APE, APE1, APEX, APX, HAP1, REF1
EC: 4.2.99.18 (PDB Primary Data), 3.1 (UniProt)
Find proteins for P27695 (Homo sapiens)
Explore P27695 
Go to UniProtKB:  P27695
NIH Common Fund Data Resources
PHAROS:  P27695
GTEx:  ENSG00000100823
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*CP*TP*AP*CP*(3DR)P*GP*AP*TP*CP*G)-3')U, X11N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP*C)-3')V, Y11N/A
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.95 Å
      • R-Value Free: 0.312 
      • R-Value Work: 0.190 
      • R-Value Observed: 0.190 
      • Space Group: I 41
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 122.85α = 90
      b = 122.85β = 90
      c = 107.07γ = 90
      Software Package:
      Software NamePurpose
      AMoREphasing
      X-PLORrefinement
      DENZOdata reduction
      SCALEPACKdata scaling

      Structure Validation

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      View more in-depth experimental data

      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2000-02-02
        Type: Initial release
      • Version 1.1: 2008-04-01
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance