5J3P

Crystal structure of the catalytic domain of human tyrosyl DNA phosphodiesterase 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.258 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mode of action of DNA-competitive small molecule inhibitors of tyrosyl DNA phosphodiesterase 2.

Hornyak, P.Askwith, T.Walker, S.Komulainen, E.Paradowski, M.Pennicott, L.E.Bartlett, E.J.Brissett, N.C.Raoof, A.Watson, M.Jordan, A.M.Ogilvie, D.J.Ward, S.E.Atack, J.R.Pearl, L.H.Caldecott, K.W.Oliver, A.W.

(2016) Biochem J 473: 1869-1879

  • DOI: 10.1042/BCJ20160180
  • Primary Citation of Related Structures:  
    5J3Z, 5J42, 5J3P, 5J3S

  • PubMed Abstract: 
  • Tyrosyl-DNA phosphodiesterase 2 (TDP2) is a 5'-tyrosyl DNA phosphodiesterase important for the repair of DNA adducts generated by non-productive (abortive) activity of topoisomerase II (TOP2). TDP2 facilitates therapeutic resistance to topoisomerase ...

    Tyrosyl-DNA phosphodiesterase 2 (TDP2) is a 5'-tyrosyl DNA phosphodiesterase important for the repair of DNA adducts generated by non-productive (abortive) activity of topoisomerase II (TOP2). TDP2 facilitates therapeutic resistance to topoisomerase poisons, which are widely used in the treatment of a range of cancer types. Consequently, TDP2 is an interesting target for the development of small molecule inhibitors that could restore sensitivity to topoisomerase-directed therapies. Previous studies identified a class of deazaflavin-based molecules that showed inhibitory activity against TDP2 at therapeutically useful concentrations, but their mode of action was uncertain. We have confirmed that the deazaflavin series inhibits TDP2 enzyme activity in a fluorescence-based assay, suitable for high-throughput screen (HTS)-screening. We have gone on to determine crystal structures of these compounds bound to a 'humanized' form of murine TDP2. The structures reveal their novel mode of action as competitive ligands for the binding site of an incoming DNA substrate, and point the way to generating novel and potent inhibitors of TDP2.


    Organizational Affiliation

    Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer BN1 9RQ, U.K. laurence.pearl@sussex.ac.uk k.w.caldecott@sussex.ac.uk antony.oliver@sussex.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosyl-DNA phosphodiesterase 2AB253Homo sapiensMutation(s): 1 
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.258 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.545α = 90
b = 92.545β = 90
c = 119.075γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC302/A14532
Cancer Research UKUnited KingdomC6563/A16771
Cancer Research UKUnited KingdomC480/A11411

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-07-06
    Changes: Database references