5TVQ

Mouse Tdp2 catalytic domain bound to SUMO2

PDB DOI: https://doi.org/10.2210/pdb5TVQ/pdb

Classification: HYDROLASE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-11-09 Released: 2017-09-27
Deposition Author(s): Schellenberg, M.J., Williams, R.S.
Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.231
R-Value Work: 0.186
R-Value Observed: 0.188

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 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

PubMed: 28912134 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 38.84 kDa
Atom Count: 2,665
Modelled Residue Count: 328
Deposited Residue Count: 342
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosyl-DNA phosphodiesterase 2	A	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9JJX7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ubiquitin-related modifier 2	B	86	Mus musculus	Mutation(s): 0 Gene Names: Sumo2, Smt3b, Smt3h2
UniProt
Find proteins for P61957 (Mus musculus) Explore P61957 Go to UniProtKB: P61957
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61957
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.231
R-Value Work: 0.186
R-Value Observed: 0.188
Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.838	α = 90
b = 106.838	β = 90
c = 56.585	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-09-27

Deposition Author(s):

Schellenberg, M.J.

Williams, R.S.

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

Revision History (Full details and data files)

Version 1.0: 2017-09-27
Type: Initial release
Version 1.1: 2017-10-11
Changes: Database references
Version 1.2: 2019-12-18
Changes: Author supporting evidence
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description