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: https://doi.org/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

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosyl-DNA phosphodiesterase 2256Mus musculusMutation(s): 0 
Gene Names: Tdp2, Ttrap
EC: 3.1.4
UniProt
Find proteins for Q9JJX7 (Mus musculus)
Explore Q9JJX7 
Go to UniProtKB:  Q9JJX7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JJX7
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Small ubiquitin-related modifier 2E [auth Q]81Mus musculusMutation(s): 0 
Gene Names: Sumo2, Smt3b, Smt3h2
UniProt
Find proteins for P61957 (Mus musculus)
Explore P61957 
Go to UniProtKB:  P61957
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61957
Protein Feature View
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')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],
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],
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

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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