5GWI image
Deposition Date 2016-09-12
Release Date 2017-08-23
Last Version Date 2024-11-20
Entry Detail
PDB ID:
5GWI
Title:
Structure of a Human topoisomerase IIbeta fragment in complex with DNA and E7873R
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.74 Å
R-Value Free:
0.25
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:DNA topoisomerase 2-beta
Gene (Uniprot):TOP2B
Chain IDs:A, B
Chain Length:803
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
Chain IDs:C, E
Chain Length:8
Number of Molecules:2
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')
Chain IDs:D, F
Chain Length:12
Number of Molecules:2
Biological Source:synthetic construct
Primary Citation
Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry
Nucleic Acids Res. 45 10861 10871 (2017)
PMID: 28977631 DOI: 10.1093/nar/gkx742

Abstact

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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Primary Citation of related structures