5TVQ

Mouse Tdp2 catalytic domain bound to SUMO2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.186 

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:  

  • 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-link ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosyl-DNA phosphodiesterase 2
A
256Mus musculusMutation(s): 0 
Gene Names: Tdp2 (Ttrap)
EC: 3.1.4.-
Find proteins for Q9JJX7 (Mus musculus)
Go to UniProtKB:  Q9JJX7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Small ubiquitin-related modifier 2
B
86Mus musculusMutation(s): 0 
Gene Names: Sumo2 (Smt3b, Smt3h2)
Find proteins for P61957 (Mus musculus)
Go to UniProtKB:  P61957
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.186 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 106.838α = 90.00
b = 106.838β = 90.00
c = 56.585γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health SciencesUnited StatesZ01ES102765

Revision History 

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2017-10-11
    Type: Database references