6Q00

TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.112 
  • R-Value Work: 0.095 
  • R-Value Observed: 0.096 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Ubiquitin stimulated reversal of topoisomerase 2 DNA-protein crosslinks by TDP2.

Schellenberg, M.J.Appel, C.D.Riccio, A.A.Butler, L.R.Krahn, J.M.Liebermann, J.A.Cortes-Ledesma, F.Williams, R.S.

(2020) Nucleic Acids Res 48: 6310-6325

  • DOI: 10.1093/nar/gkaa318
  • Primary Citation of Related Structures:  
    6Q00, 6Q01

  • PubMed Abstract: 
  • Tyrosyl-DNA phosphodiesterase 2 (TDP2) reverses Topoisomerase 2 DNA-protein crosslinks (TOP2-DPCs) in a direct-reversal pathway licensed by ZATTZNF451 SUMO2 E3 ligase and SUMOylation of TOP2. TDP2 also binds ubiquitin (Ub), but how Ub regulates TDP2 ...

    Tyrosyl-DNA phosphodiesterase 2 (TDP2) reverses Topoisomerase 2 DNA-protein crosslinks (TOP2-DPCs) in a direct-reversal pathway licensed by ZATTZNF451 SUMO2 E3 ligase and SUMOylation of TOP2. TDP2 also binds ubiquitin (Ub), but how Ub regulates TDP2 functions is unknown. Here, we show that TDP2 co-purifies with K63 and K27 poly-Ubiquitinated cellular proteins independently of, and separately from SUMOylated TOP2 complexes. Poly-ubiquitin chains of ≥ Ub3 stimulate TDP2 catalytic activity in nuclear extracts and enhance TDP2 binding of DNA-protein crosslinks in vitro. X-ray crystal structures and small-angle X-ray scattering analysis of TDP2-Ub complexes reveal that the TDP2 UBA domain binds K63-Ub3 in a 1:1 stoichiometric complex that relieves a UBA-regulated autoinhibitory state of TDP2. Our data indicates that that poly-Ub regulates TDP2-catalyzed TOP2-DPC removal, and TDP2 single nucleotide polymorphisms can disrupt the TDP2-Ubiquitin interface.


    Organizational Affiliation

    Structural Cell Biology Group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, US Department of Health and Human Services, Research Triangle Park, NC 27709, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinA76Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
NIH Common Fund Data Resources
PHAROS  P0CG48
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosyl-DNA phosphodiesterase 2B45Homo sapiensMutation(s): 0 
Gene Names: TDP2EAP2TTRAPAD-022
EC: 3.1.4
Find proteins for O95551 (Homo sapiens)
Explore O95551 
Go to UniProtKB:  O95551
NIH Common Fund Data Resources
PHAROS  O95551
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download Ideal Coordinates CCD File 
B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
BL-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.112 
  • R-Value Work: 0.095 
  • R-Value Observed: 0.096 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.742α = 90
b = 48.742β = 90
c = 50.421γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
HKL-2000data collection
PDB_EXTRACTdata extraction

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 

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-13
    Changes: Database references
  • Version 1.2: 2020-06-24
    Changes: Database references