RCSB PDB - 5GWI: Structure of a Human topoisomerase IIbeta fragment in complex with DNA and E7873R

 5GWI

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted N2NClick on this verticalbar to view detailsBest fitted N2RClick on this verticalbar to view details

This is version 2.2 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: https://doi.org/10.1093/nar/gkx742
  • Primary Citation of Related Structures:  
    5GWI, 5GWJ, 5GWK

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA topoisomerase 2-beta
A, B
803Homo sapiensMutation(s): 0 
Gene Names: TOP2B
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q02880 (Homo sapiens)
Explore Q02880 
Go to UniProtKB:  Q02880
PHAROS:  Q02880
GTEx:  ENSG00000077097 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02880
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N2N
Query on N2N

Download Ideal Coordinates CCD File 
H [auth A],
M [auth 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
N2R
Query on N2R

Download Ideal Coordinates CCD File 
G [auth A],
K [auth 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
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
L [auth B]
N [auth D]
O [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.788α = 90
b = 176.966β = 112.3
c = 94.528γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted N2NClick on this verticalbar to view detailsBest fitted N2RClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Database references, Source and taxonomy
  • Version 2.0: 2017-12-13
    Changes: Non-polymer description, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.2: 2024-11-20
    Changes: Structure summary