5TVP

SUMO2 bound to Mouse Tdp2 catalytic domain with a 5'-phosphorylated DNA ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

ZATT (ZNF451)-mediated resolution of topoisomerase 2 DNA-protein cross-links.

Schellenberg, M.J.Lieberman, J.A.Herrero-Ruiz, A.Butler, L.R.Williams, J.G.Munoz-Cabello, A.M.Mueller, G.A.London, R.E.Cortes-Ledesma, F.Williams, R.S.

(2017) Science 357: 1412-1416

  • DOI: 10.1126/science.aam6468
  • Primary Citation of Related Structures:  
    5TVP, 5TVQ

  • PubMed Abstract: 
  • Topoisomerase 2 (TOP2) DNA transactions proceed via formation of the TOP2 cleavage complex (TOP2cc), a covalent enzyme-DNA reaction intermediate that is vulnerable to trapping by potent anticancer TOP2 drugs. How genotoxic TOP2 DNA-protein cross-links are resolved is unclear ...

    Topoisomerase 2 (TOP2) DNA transactions proceed via formation of the TOP2 cleavage complex (TOP2cc), a covalent enzyme-DNA reaction intermediate that is vulnerable to trapping by potent anticancer TOP2 drugs. How genotoxic TOP2 DNA-protein cross-links are resolved is unclear. We found that the SUMO (small ubiquitin-related modifier) ligase ZATT (ZNF451) is a multifunctional DNA repair factor that controls cellular responses to TOP2 damage. ZATT binding to TOP2cc facilitates a proteasome-independent tyrosyl-DNA phosphodiesterase 2 (TDP2) hydrolase activity on stalled TOP2cc. The ZATT SUMO ligase activity further promotes TDP2 interactions with SUMOylated TOP2, regulating efficient TDP2 recruitment through a "split-SIM" SUMO2 engagement platform. These findings uncover a ZATT-TDP2-catalyzed and SUMO2-modulated pathway for direct resolution of TOP2cc.


    Organizational Affiliation

    Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC 27709, USA. felipe.cortes@cabimer.es williamsrs@niehs.nih.gov.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosyl-DNA phosphodiesterase 2L [auth A], J [auth B], F [auth E], H [auth G], A [auth I], N [auth K], P [auth M], C [auth O]256Mus musculusMutation(s): 0 
Gene Names: Tdp2Ttrap
EC: 3.1.4
UniProt
Find proteins for Q9JJX7 (Mus musculus)
Explore Q9JJX7 
Go to UniProtKB:  Q9JJX7
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Small ubiquitin-related modifier 2E [auth Q]81Mus musculusMutation(s): 0 
Gene Names: Sumo2Smt3bSmt3h2
UniProt
Find proteins for P61957 (Mus musculus)
Explore P61957 
Go to UniProtKB:  P61957
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')K [auth C], M [auth D], G [auth F], I [auth H], B [auth J], O [auth L], Q [auth N], D [auth P]9Homo sapiens
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PO4
    Query on PO4

    Download Ideal Coordinates CCD File 
    AA [auth E] , BA [auth G] , GA [auth B] , JA [auth A] , LA [auth K] , OA [auth M] , R [auth I] , U [auth O] , 
    AA [auth E],  BA [auth G],  GA [auth B],  JA [auth A],  LA [auth K],  OA [auth M],  R [auth I],  U [auth O],  Y [auth E]
    PHOSPHATE ION
    O4 P
    NBIIXXVUZAFLBC-UHFFFAOYSA-K
     Ligand Interaction
    EDO
    Query on EDO

    Download Ideal Coordinates CCD File 
    CA [auth G] , DA [auth G] , EA [auth G] , FA [auth G] , HA [auth B] , KA [auth A] , MA [auth K] , NA [auth K] , 
    CA [auth G],  DA [auth G],  EA [auth G],  FA [auth G],  HA [auth B],  KA [auth A],  MA [auth K],  NA [auth K],  S [auth I],  T [auth I],  V [auth O],  W [auth O],  X [auth O]
    1,2-ETHANEDIOL
    C2 H6 O2
    LYCAIKOWRPUZTN-UHFFFAOYSA-N
     Ligand Interaction
    CL
    Query on CL

    Download Ideal Coordinates CCD File 
    IA [auth B], PA [auth M], Z [auth E]CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.40 Å
    • R-Value Free: 0.233 
    • R-Value Work: 0.191 
    • R-Value Observed: 0.193 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 106.547α = 90
    b = 113.772β = 91.52
    c = 125.434γ = 90
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    PHENIXrefinement
    PDB_EXTRACTdata extraction
    PHASERphasing

    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  (Full details and data files)

    • Version 1.0: 2017-10-11
      Type: Initial release
    • Version 1.1: 2019-12-18
      Changes: Author supporting evidence