5INL

Mouse Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex with deoxyadenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.131 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2.

Schellenberg, M.J.Perera, L.Strom, C.N.Waters, C.A.Monian, B.Appel, C.D.Vilas, C.K.Williams, J.G.Ramsden, D.A.Williams, R.S.

(2016) Nucleic Acids Res 44: 3829-3844

  • DOI: 10.1093/nar/gkw228
  • Primary Citation of Related Structures:  
    5HT2, 5INK, 5INM, 5INL, 5INO, 5INN, 5INQ, 5INP

  • PubMed Abstract: 
  • Mammalian Tyrosyl-DNA phosphodiesterase 2 (Tdp2) reverses Topoisomerase 2 (Top2) DNA-protein crosslinks triggered by Top2 engagement of DNA damage or poisoning by anticancer drugs. Tdp2 deficiencies are linked to neurological disease and cellular sen ...

    Mammalian Tyrosyl-DNA phosphodiesterase 2 (Tdp2) reverses Topoisomerase 2 (Top2) DNA-protein crosslinks triggered by Top2 engagement of DNA damage or poisoning by anticancer drugs. Tdp2 deficiencies are linked to neurological disease and cellular sensitivity to Top2 poisons. Herein, we report X-ray crystal structures of ligand-free Tdp2 and Tdp2-DNA complexes with alkylated and abasic DNA that unveil a dynamic Tdp2 active site lid and deep substrate binding trench well-suited for engaging the diverse DNA damage triggers of abortive Top2 reactions. Modeling of a proposed Tdp2 reaction coordinate, combined with mutagenesis and biochemical studies support a single Mg(2+)-ion mechanism assisted by a phosphotyrosyl-arginine cation-π interface. We further identify a Tdp2 active site SNP that ablates Tdp2 Mg(2+) binding and catalytic activity, impairs Tdp2 mediated NHEJ of tyrosine blocked termini, and renders cells sensitive to the anticancer agent etoposide. Collectively, our results provide a structural mechanism for Tdp2 engagement of heterogeneous DNA damage that causes Top2 poisoning, and indicate that evaluation of Tdp2 status may be an important personalized medicine biomarker informing on individual sensitivities to chemotherapeutic Top2 poisons.


    Organizational Affiliation

    Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA williamsrs@niehs.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 (5'-D(P*AP*CP*GP*AP*AP*TP*TP*CP*G)-3')C, D9Homo sapiens
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    EPE
    Query on EPE

    Download CCD File 
    B
    4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
    C8 H18 N2 O4 S
    JKMHFZQWWAIEOD-UHFFFAOYSA-N
     Ligand Interaction
    PEG
    Query on PEG

    Download CCD File 
    B
    DI(HYDROXYETHYL)ETHER
    C4 H10 O3
    MTHSVFCYNBDYFN-UHFFFAOYSA-N
     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: 1.55 Å
    • R-Value Free: 0.168 
    • R-Value Work: 0.129 
    • R-Value Observed: 0.131 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 54.903α = 90
    b = 69.051β = 90
    c = 167.805γ = 90
    Software Package:
    Software NamePurpose
    SCALEPACKdata scaling
    PHENIXrefinement
    PDB_EXTRACTdata extraction
    DENZOdata reduction
    PHENIXphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1Z01ES102765

    Revision History 

    • Version 1.0: 2016-04-27
      Type: Initial release
    • Version 1.1: 2016-05-18
      Changes: Database references
    • Version 1.2: 2017-09-20
      Changes: Author supporting evidence, Database references, Derived calculations
    • Version 1.3: 2019-12-18
      Changes: Author supporting evidence