1DE9

HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

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

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 ...

    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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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
MAJOR APURINIC/APYRIMIDINIC ENDONUCLEASEAB276Homo sapiensMutation(s): 0 
Gene Names: APEX1APEAPE1APEXAPXHAP1REF1
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
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-d(*CP*TP*AP*C)-3'U, X4N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-d(P*(3DR)P*GP*AP*TP*C)-3'V, Y5N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        5'-d(*GP*AP*TP*CP*GP*GP*TP*AP*G)-3'W, Z9N/A
        Small Molecules
        Ligands 1 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        MN
        Query on MN

        Download CCD File 
        A, B
        MANGANESE (II) ION
        Mn
        WAEMQWOKJMHJLA-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 3.00 Å
        • R-Value Free: 0.274 
        • R-Value Work: 0.183 
        • R-Value Observed: 0.183 
        • Space Group: P 21 21 21
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 90.06α = 90
        b = 98.35β = 90
        c = 101.05γ = 90
        Software Package:
        Software NamePurpose
        DENZOdata reduction
        SCALEPACKdata scaling
        AMoREphasing
        X-PLORrefinement

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History 

        • Version 1.0: 2000-02-02
          Type: Initial release
        • Version 1.1: 2008-04-27
          Changes: Version format compliance
        • Version 1.2: 2011-07-13
          Changes: Version format compliance