5TVP

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

• PDB DOI: https://doi.org/10.2210/pdb5TVP/pdb
• NAKB: 5TVP

• Classification: hydrolase/dna
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-11-09 Released: 2017-10-11 
• Deposition Author(s): Schellenberg, M.J., Williams, R.S.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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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 

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

• PubMed: 28912134 
• 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. 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.

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Organizational Affiliation: 

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC 27709, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 264.1 kDa 
• Atom Count: 18,735 
• Modelled Residue Count: 2,147 
• Deposited Residue Count: 2,201 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosyl-DNA phosphodiesterase 2	A [auth I], C [auth O], F [auth E], H [auth G], J [auth B], L [auth A], N [auth K], P [auth M]	256	Mus musculus	Mutation(s): 0  Gene Names: Tdp2, Ttrap EC: 3.1.4
UniProt
Find proteins for Q9JJX7 (Mus musculus) Explore Q9JJX7  Go to UniProtKB:  Q9JJX7

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ubiquitin-related modifier 2	E [auth Q]	81	Mus musculus	Mutation(s): 0  Gene Names: Sumo2, Smt3b, Smt3h2
UniProt
Find proteins for P61957 (Mus musculus) Explore P61957  Go to UniProtKB:  P61957

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')	B [auth J], D [auth P], G [auth F], I [auth H], K [auth C], M [auth D], O [auth L], Q [auth N]	9	Homo sapiens

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	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
EDO	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
CL	IA [auth B], PA [auth M], Z [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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 = 106.547	α = 90
b = 113.772	β = 91.52
c = 125.434	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-10-11 
Deposition Author(s): Schellenberg, M.J., Williams, R.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	1Z01ES102765

Revision History  

• Version 1.0: 2017-10-11
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description