5GWI

Structure of a Human topoisomerase IIbeta fragment in complex with DNA and E7873R


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.737 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry

Wang, Y.R.Chen, S.F.Wu, C.C.Liao, Y.W.Lin, T.S.Liu, K.T.Chen, Y.S.Li, T.K.Chien, T.C.Chan, N.L.

(2017) Nucleic Acids Res. 45: 10861-10871

  • DOI: 10.1093/nar/gkx742
  • Primary Citation of Related Structures:  5GWK, 5GWJ

  • PubMed Abstract: 
  • Human type II topoisomerase (Top2) isoforms, hTop2α and hTop2β, are targeted by some of the most successful anticancer drugs. These drugs induce Top2-mediated DNA cleavage to trigger cell-death pathways. The potency of these drugs correlates positive ...

    Human type II topoisomerase (Top2) isoforms, hTop2α and hTop2β, are targeted by some of the most successful anticancer drugs. These drugs induce Top2-mediated DNA cleavage to trigger cell-death pathways. The potency of these drugs correlates positively with their efficacy in stabilizing the enzyme-mediated DNA breaks. Structural analysis of hTop2α and hTop2β revealed the presence of methionine residues in the drug-binding pocket, we therefore tested whether a tighter Top2-drug association may be accomplished by introducing a methionine-reactive Pt2+ into a drug to further stabilize the DNA break. Herein, we synthesized an organoplatinum compound, etoplatin-N2β, by replacing the methionine-juxtaposing group of the drug etoposide with a cis-dichlorodiammineplatinum(II) moiety. Compared to etoposide, etoplatin-N2β more potently inhibits both human Top2s. While the DNA breaks arrested by etoposide can be rejoined, those captured by etoplatin-N2β are practically irreversible. Crystallographic analyses of hTop2β complexed with DNA and etoplatin-N2β demonstrate coordinate bond formation between Pt2+ and a flanking methionine. Notably, this stable coordinate tether can be loosened by disrupting the structural integrity of drug-binding pocket, suggesting that Pt2+ coordination chemistry may allow for the development of potent inhibitors with protein conformation-dependent reversibility. This approach may be exploited to achieve isoform-specific targeting of human Top2s.


    Organizational Affiliation

    Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA topoisomerase 2-beta
A, B
803Homo sapiensGene Names: TOP2B
EC: 5.99.1.3
Find proteins for Q02880 (Homo sapiens)
Go to Gene View: TOP2B
Go to UniProtKB:  Q02880
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')C,E8synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')D,F12synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N2N
Query on N2N

Download SDF File 
Download CCD File 
A, B
dichloro{4,5-di(amino-kappaN)-N-[9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydro-2H-furo[3',4':6,7]naphtho[2,3-d][1,3]dioxol-5-yl]pentanamide}platinum
C26 H31 Cl2 N3 O8 Pt
PTKKCRGGEZZAPV-BFZFYWOISA-L
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
N2R
Query on N2R

Download SDF File 
Download CCD File 
A, B
dichloro{4,5-di(amino-kappaN)-N-[9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydro-2H-furo[3',4':6,7]naphtho[2,3-d][1,3]dioxol-5-yl]pentanamide}platinum
C26 H31 Cl2 N3 O8 Pt
PTKKCRGGEZZAPV-FTKFZVBUSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.737 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 79.788α = 90.00
b = 176.966β = 112.30
c = 94.528γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Database references, Source and taxonomy
  • Version 2.0: 2017-12-13
    Type: Non-polymer description, Structure summary