4GZ2

Mus Musculus Tdp2 excluded ssDNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2.

Schellenberg, M.J.Appel, C.D.Adhikari, S.Robertson, P.D.Ramsden, D.A.Williams, R.S.

(2012) Nat Struct Mol Biol 19: 1363-1371

  • DOI: 10.1038/nsmb.2418
  • Primary Citation of Related Structures:  
    4GYZ, 4GZ0, 4GZ1, 4GZ2

  • PubMed Abstract: 
  • The topoisomerase II (topo II) DNA incision-and-ligation cycle can be poisoned (for example following treatment with cancer chemotherapeutics) to generate cytotoxic DNA double-strand breaks (DSBs) with topo II covalently conjugated to DNA. Tyrosyl-DN ...

    The topoisomerase II (topo II) DNA incision-and-ligation cycle can be poisoned (for example following treatment with cancer chemotherapeutics) to generate cytotoxic DNA double-strand breaks (DSBs) with topo II covalently conjugated to DNA. Tyrosyl-DNA phosphodiesterase 2 (Tdp2) protects genomic integrity by reversing 5'-phosphotyrosyl-linked topo II-DNA adducts. Here, X-ray structures of mouse Tdp2-DNA complexes reveal that Tdp2 β-2-helix-β DNA damage-binding 'grasp', helical 'cap' and DNA lesion-binding elements fuse to form an elongated protein-DNA conjugate substrate-interaction groove. The Tdp2 DNA-binding surface is highly tailored for engagement of 5'-adducted single-stranded DNA ends and restricts nonspecific endonucleolytic or exonucleolytic processing. Structural, mutational and functional analyses support a single-metal ion catalytic mechanism for the exonuclease-endonuclease-phosphatase (EEP) nuclease superfamily and establish a molecular framework for targeted small-molecule blockade of Tdp2-mediated resistance to anticancer topoisomerase drugs.


    Organizational Affiliation

    Laboratory of Structural Biology, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, North Carolina, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosyl-DNA phosphodiesterase 2AB255Mus musculusMutation(s): 0 
Gene Names: Tdp2Ttrap
EC: 3.1.4
Find proteins for Q9JJX7 (Mus musculus)
Explore Q9JJX7 
Go to UniProtKB:  Q9JJX7
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*AP*TP*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')C, D12N/A
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    FMT
    Query on FMT

    Download CCD File 
    A, B
    FORMIC ACID
    C H2 O2
    BDAGIHXWWSANSR-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.85 Å
    • R-Value Free: 0.245 
    • R-Value Work: 0.205 
    • R-Value Observed: 0.207 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 60.483α = 90
    b = 42.972β = 95.89
    c = 107.951γ = 90
    Software Package:
    Software NamePurpose
    SCALEPACKdata scaling
    PHENIXrefinement
    PDB_EXTRACTdata extraction
    HKL-2000data collection
    DENZOdata reduction
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2012-10-31
      Type: Initial release
    • Version 1.1: 2012-11-21
      Changes: Database references
    • Version 1.2: 2012-11-28
      Changes: Database references
    • Version 1.3: 2013-01-02
      Changes: Database references
    • Version 1.4: 2020-07-22
      Changes: Database references, Derived calculations