4G0W

Human topoisomerase iibeta in complex with DNA and ametantrone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

On the structural basis and design guidelines for type II topoisomerase-targeting anticancer drugs

Wu, C.C.Li, Y.C.Wang, Y.R.Li, T.K.Chan, N.L.

(2013) Nucleic Acids Res 41: 10630-10640

  • DOI: 10.1093/nar/gkt828
  • Primary Citation of Related Structures:  
    4G0U, 4G0V, 4G0W, 4J3N

  • PubMed Abstract: 
  • Type II topoisomerases (Top2s) alter DNA topology via the formation of an enzyme-DNA adduct termed cleavage complex, which harbors a transient double-strand break in one DNA to allow the passage of another. Agents targeting human Top2s are clinically act ...

    Type II topoisomerases (Top2s) alter DNA topology via the formation of an enzyme-DNA adduct termed cleavage complex, which harbors a transient double-strand break in one DNA to allow the passage of another. Agents targeting human Top2s are clinically active anticancer drugs whose trapping of Top2-mediated DNA breakage effectively induces genome fragmentation and cell death. To understand the structural basis of this drug action, we previously determined the structure of human Top2 β-isoform forming a cleavage complex with the drug etoposide and DNA, and described the insertion of drug into DNA cleavage site and drug-induced decoupling of catalytic groups. By developing a post-crystallization drug replacement procedure that simplifies structural characterization of drug-stabilized cleavage complexes, we have extended the analysis toward other structurally distinct drugs, m-AMSA and mitoxantrone. Besides the expected drug intercalation, a switch in ribose puckering in the 3'-nucleotide of the cleavage site was robustly observed in the new structures, representing a new mechanism for trapping the Top2 cleavage complex. Analysis of drug-binding modes and the conformational landscapes of the drug-binding pockets provide rationalization of the drugs' structural-activity relationships and explain why Top2 mutants exhibit differential effects toward each drug. Drug design guidelines were proposed to facilitate the development of isoform-specific Top2-targeting anticancer agents.


    Organizational Affiliation

    Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan, Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan, Department and Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan and Center for Biotechnology, National Taiwan University, Taipei 106, Taiwan.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase 2-beta AB803Homo sapiensMutation(s): 0 
Gene Names: TOP2B
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
Find proteins for Q02880 (Homo sapiens)
Explore Q02880 
Go to UniProtKB:  Q02880
NIH Common Fund Data Resources
PHAROS:  Q02880
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')C, E8N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')D, F12N/A
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.70 Å
      • R-Value Free: 0.215 
      • R-Value Work: 0.165 
      • R-Value Observed: 0.168 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 80.662α = 90
      b = 176.424β = 112.04
      c = 93.635γ = 90
      Software Package:
      Software NamePurpose
      Blu-Icedata collection
      PHENIXmodel building
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling
      PHENIXphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2013-07-17
        Type: Initial release
      • Version 1.1: 2013-10-02
        Changes: Database references
      • Version 1.2: 2014-03-12
        Changes: Database references