5DFH

Human APE1 mismatch product complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Capturing snapshots of APE1 processing DNA damage.

Freudenthal, B.D.Beard, W.A.Cuneo, M.J.Dyrkheeva, N.S.Wilson, S.H.

(2015) Nat Struct Mol Biol 22: 924-931

  • DOI: 10.1038/nsmb.3105
  • Primary Citation of Related Structures:  
    5DG0, 5DFH, 5DFJ, 5DFI, 5DFF

  • PubMed Abstract: 
  • DNA apurinic-apyrimidinic (AP) sites are prevalent noncoding threats to genomic stability and are processed by AP endonuclease 1 (APE1). APE1 incises the AP-site phosphodiester backbone, generating a DNA-repair intermediate that is potentially cytoto ...

    DNA apurinic-apyrimidinic (AP) sites are prevalent noncoding threats to genomic stability and are processed by AP endonuclease 1 (APE1). APE1 incises the AP-site phosphodiester backbone, generating a DNA-repair intermediate that is potentially cytotoxic. The molecular events of the incision reaction remain elusive, owing in part to limited structural information. We report multiple high-resolution human APE1-DNA structures that divulge new features of the APE1 reaction, including the metal-binding site, the nucleophile and the arginine clamps that mediate product release. We also report APE1-DNA structures with a T-G mismatch 5' to the AP site, representing a clustered lesion occurring in methylated CpG dinucleotides. These structures reveal that APE1 molds the T-G mismatch into a unique Watson-Crick-like geometry that distorts the active site, thus reducing incision. These snapshots provide mechanistic clarity for APE1 while affording a rational framework to manipulate biological responses to DNA damage.


    Organizational Affiliation

    Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Research Triangle Park, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-(apurinic or apyrimidinic site) lyaseAB276Homo sapiensMutation(s): 0 
Gene Names: APEX1APEAPE1APEXAPXHAP1REF1
EC: 3.1 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
Find proteins for P27695 (Homo sapiens)
Explore P27695 
Go to UniProtKB:  P27695
NIH Common Fund Data Resources
PHAROS  P27695
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')D11synthetic construct
    Find similar nucleic acids by: 
    (by identity cutoff)  |  Structure
    Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')V21synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*T)-3')C10synthetic construct
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      EDO
      Query on EDO

      Download CCD File 
      A
      1,2-ETHANEDIOL
      C2 H6 O2
      LYCAIKOWRPUZTN-UHFFFAOYSA-N
       Ligand Interaction
      MG
      Query on MG

      Download CCD File 
      A
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.95 Å
      • R-Value Free: 0.219 
      • R-Value Work: 0.179 
      • R-Value Observed: 0.180 
      • Space Group: P 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 44.434α = 83.86
      b = 61.603β = 78.76
      c = 72.277γ = 88.19
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-3000data reduction
      HKL-3000data scaling

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

      Revision History 

      • Version 1.0: 2015-10-14
        Type: Initial release
      • Version 1.1: 2015-11-11
        Changes: Database references
      • Version 1.2: 2015-12-02
        Changes: Database references
      • Version 1.3: 2017-09-20
        Changes: Author supporting evidence, Derived calculations
      • Version 1.4: 2019-12-25
        Changes: Author supporting evidence