5GWI | pdb_00005gwi

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

• PDB DOI: https://doi.org/10.2210/pdb5GWI/pdb
• NAKB: 5GWI

• Classification: ISOMERASE/DNA/ISOMERASE INHIBITOR
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-12 Released: 2017-08-23 
• Deposition Author(s): Wang, Y.R., Chen, S.F., Wu, C.C., Chan, N.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 
  0.253 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

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

• PubMed: 28977631 
• DOI: https://doi.org/10.1093/nar/gkx742
• Primary Citation 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.

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Organizational Affiliation: 
• Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan.
Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan.
Department and Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan.
Center for Biotechnology, National Taiwan University, Taipei 106, Taiwan.
Department of Chemistry, National Taiwan Normal University, Taipei 116, Taiwan.
Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 199.3 kDa 
• Atom Count: 12,019 
• Modeled Residue Count: 1,382 
• Deposited Residue Count: 1,646 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 2-beta	A, B	803	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')	C, E	8	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')	D, F	12	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N2R	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
N2N	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
MG	I [auth A], J [auth A], L [auth B], N [auth D], O [auth E], P [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free:  0.253 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.788	α = 90
b = 176.966	β = 112.3
c = 94.528	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-23 
Deposition Author(s): Wang, Y.R., Chen, S.F., Wu, C.C., Chan, N.L.

Revision History  

• 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