4PUQ

Mus Musculus Tdp2 reaction product complex with 5'-phosphorylated RNA/DNA, glycerol, and Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.131 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Proteolytic Degradation of Topoisomerase II (Top2) Enables the Processing of Top2DNA and Top2RNA Covalent Complexes by Tyrosyl-DNA-Phosphodiesterase 2 (TDP2).

Gao, R.Schellenberg, M.J.Huang, S.Y.Abdelmalak, M.Marchand, C.Nitiss, K.C.Nitiss, J.L.Williams, R.S.Pommier, Y.

(2014) J Biol Chem 289: 17960-17969

  • DOI: 10.1074/jbc.M114.565374
  • Primary Citation of Related Structures:  
    4PUQ

  • PubMed Abstract: 
  • Eukaryotic type II topoisomerases (Top2α and Top2β) are homodimeric enzymes; they are essential for altering DNA topology by the formation of normally transient double strand DNA cleavage. Anticancer drugs (etoposide, doxorubicin, and mitoxantrone) a ...

    Eukaryotic type II topoisomerases (Top2α and Top2β) are homodimeric enzymes; they are essential for altering DNA topology by the formation of normally transient double strand DNA cleavage. Anticancer drugs (etoposide, doxorubicin, and mitoxantrone) and also Top2 oxidation and DNA helical alterations cause potentially irreversible Top2·DNA cleavage complexes (Top2cc), leading to Top2-linked DNA breaks. Top2cc are the therapeutic mechanism for killing cancer cells. Yet Top2cc can also generate recombination, translocations, and apoptosis in normal cells. The Top2 protein-DNA covalent complexes are excised (in part) by tyrosyl-DNA-phosphodiesterase 2 (TDP2/TTRAP/EAP2/VPg unlinkase). In this study, we show that irreversible Top2cc induced in suicidal substrates are not processed by TDP2 unless they first undergo proteolytic processing or denaturation. We also demonstrate that TDP2 is most efficient when the DNA attached to the tyrosyl is in a single-stranded configuration and that TDP2 can efficiently remove a tyrosine linked to a single misincorporated ribonucleotide or to polyribonucleotides, which expands the TDP2 catalytic profile with RNA substrates. The 1.6-Å resolution crystal structure of TDP2 bound to a substrate bearing a 5'-ribonucleotide defines a mechanism through which RNA can be accommodated in the TDP2 active site, albeit in a strained conformation.


    Organizational Affiliation

    From the Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892, pommier@nih.gov.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosyl-DNA phosphodiesterase 2AB256Mus 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/RNA hybridC, D9N/A
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GOL
    Query on GOL

    Download CCD File 
    B, D
    GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N
     Ligand Interaction
    ACT
    Query on ACT

    Download CCD File 
    D
    ACETATE ION
    C2 H3 O2
    QTBSBXVTEAMEQO-UHFFFAOYSA-M
     Ligand Interaction
    MG
    Query on MG

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

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.60 Å
    • R-Value Free: 0.171 
    • R-Value Work: 0.129 
    • R-Value Observed: 0.131 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 54.828α = 90
    b = 69.258β = 90
    c = 167.107γ = 90
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    PHENIXrefinement
    PDB_EXTRACTdata extraction
    SERGUIdata collection
    PHENIXphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2014-05-14
      Type: Initial release
    • Version 1.1: 2014-06-25
      Changes: Database references
    • Version 1.2: 2014-07-23
      Changes: Database references