5INO

Human Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.205 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2.

Schellenberg, M.J.Perera, L.Strom, C.N.Waters, C.A.Monian, B.Appel, C.D.Vilas, C.K.Williams, J.G.Ramsden, D.A.Williams, R.S.

(2016) Nucleic Acids Res. 44: 3829-3844

  • DOI: 10.1093/nar/gkw228
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mammalian Tyrosyl-DNA phosphodiesterase 2 (Tdp2) reverses Topoisomerase 2 (Top2) DNA-protein crosslinks triggered by Top2 engagement of DNA damage or poisoning by anticancer drugs. Tdp2 deficiencies are linked to neurological disease and cellular sen ...

    Mammalian Tyrosyl-DNA phosphodiesterase 2 (Tdp2) reverses Topoisomerase 2 (Top2) DNA-protein crosslinks triggered by Top2 engagement of DNA damage or poisoning by anticancer drugs. Tdp2 deficiencies are linked to neurological disease and cellular sensitivity to Top2 poisons. Herein, we report X-ray crystal structures of ligand-free Tdp2 and Tdp2-DNA complexes with alkylated and abasic DNA that unveil a dynamic Tdp2 active site lid and deep substrate binding trench well-suited for engaging the diverse DNA damage triggers of abortive Top2 reactions. Modeling of a proposed Tdp2 reaction coordinate, combined with mutagenesis and biochemical studies support a single Mg(2+)-ion mechanism assisted by a phosphotyrosyl-arginine cation-π interface. We further identify a Tdp2 active site SNP that ablates Tdp2 Mg(2+) binding and catalytic activity, impairs Tdp2 mediated NHEJ of tyrosine blocked termini, and renders cells sensitive to the anticancer agent etoposide. Collectively, our results provide a structural mechanism for Tdp2 engagement of heterogeneous DNA damage that causes Top2 poisoning, and indicate that evaluation of Tdp2 status may be an important personalized medicine biomarker informing on individual sensitivities to chemotherapeutic Top2 poisons.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosyl-DNA phosphodiesterase 2
A, B
258Homo sapiensMutation(s): 0 
Gene Names: TDP2 (EAP2, TTRAP)
EC: 3.1.4.-
Find proteins for O95551 (Homo sapiens)
Go to Gene View: TDP2
Go to UniProtKB:  O95551
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')D,C9Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.205 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.214 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 69.663α = 90.00
b = 69.663β = 90.00
c = 120.677γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
SCALEPACKdata scaling
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 States1Z01ES102765

Revision History 

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-05-18
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Refinement description