4NDH

Human Aprataxin (Aptx) bound to DNA, AMP, and Zn - product complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Aprataxin resolves adenylated RNA-DNA junctions to maintain genome integrity.

Tumbale, P.Williams, J.S.Schellenberg, M.J.Kunkel, T.A.Williams, R.S.

(2013) Nature 506: 111-115

  • DOI: 10.1038/nature12824
  • Primary Citation of Related Structures:  
    4NDF, 4NDG, 4NDH, 4NDI

  • PubMed Abstract: 
  • Faithful maintenance and propagation of eukaryotic genomes is ensured by three-step DNA ligation reactions used by ATP-dependent DNA ligases. Paradoxically, when DNA ligases encounter nicked DNA structures with abnormal DNA termini, DNA ligase catalytic activity can generate and/or exacerbate DNA damage through abortive ligation that produces chemically adducted, toxic 5'-adenylated (5'-AMP) DNA lesions ...

    Faithful maintenance and propagation of eukaryotic genomes is ensured by three-step DNA ligation reactions used by ATP-dependent DNA ligases. Paradoxically, when DNA ligases encounter nicked DNA structures with abnormal DNA termini, DNA ligase catalytic activity can generate and/or exacerbate DNA damage through abortive ligation that produces chemically adducted, toxic 5'-adenylated (5'-AMP) DNA lesions. Aprataxin (APTX) reverses DNA adenylation but the context for deadenylation repair is unclear. Here we examine the importance of APTX to RNase-H2-dependent excision repair (RER) of a lesion that is very frequently introduced into DNA, a ribonucleotide. We show that ligases generate adenylated 5' ends containing a ribose characteristic of RNase H2 incision. APTX efficiently repairs adenylated RNA-DNA, and acting in an RNA-DNA damage response (RDDR), promotes cellular survival and prevents S-phase checkpoint activation in budding yeast undergoing RER. Structure-function studies of human APTX-RNA-DNA-AMP-Zn complexes define a mechanism for detecting and reversing adenylation at RNA-DNA junctions. This involves A-form RNA binding, proper protein folding and conformational changes, all of which are affected by heritable APTX mutations in ataxia with oculomotor apraxia 1. Together, these results indicate that accumulation of adenylated RNA-DNA may contribute to neurological disease.


    Organizational Affiliation

    Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, North Carolina 27709, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AprataxinA, B182Homo sapiensMutation(s): 0 
Gene Names: APTXAXA1
EC: 3.6.1.71 (UniProt), 3.6.1.72 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z2E3 (Homo sapiens)
Explore Q7Z2E3 
Go to UniProtKB:  Q7Z2E3
PHAROS:  Q7Z2E3
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(P*GP*TP*TP*CP*TP*AP*GP*AP*AP*C)-3'C [auth D], D [auth E], E [auth G], F [auth H]10N/A
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    AMP
    Query on AMP

    Download Ideal Coordinates CCD File 
    G [auth A], I [auth B]ADENOSINE MONOPHOSPHATE
    C10 H14 N5 O7 P
    UDMBCSSLTHHNCD-KQYNXXCUSA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    H [auth A], J [auth B]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.85 Å
    • R-Value Free: 0.196 
    • R-Value Work: 0.163 
    • R-Value Observed: 0.164 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 40.397α = 90
    b = 117.082β = 90
    c = 118.202γ = 90
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    PHENIXrefinement
    PDB_EXTRACTdata extraction
    SERGUIdata collection
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2013-12-18
      Type: Initial release
    • Version 1.1: 2014-01-15
      Changes: Database references
    • Version 1.2: 2014-02-05
      Changes: Database references