Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 98.20 kDa 
• Atom Count: 6892 
• Modelled Residue Count: 756 
• Deposited Residue Count: 836 
• Unique protein chains: 1

1PVG

Crystal Structure of the ATPase region of Saccharomyces Cerevisiae topoisomerase II

• PDB DOI: 10.2210/pdb1PVG/pdb

• Classification: ISOMERASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-06-27 Released: 2003-08-26 
• Deposition Author(s): Classen, S., Olland, S., Berger, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.241 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 

Literature

Structure of the topoisomerase II ATPase region and its mechanism of inhibition by the chemotherapeutic agent ICRF-187

Classen, S., Olland, S., Berger, J.M.

(2003) Proc Natl Acad Sci U S A 100: 10629-10634

• PubMed: 12963818 
• DOI: 10.1073/pnas.1832879100
• Primary Citation of Related Structures:  
  1PVG, 1QZR


• PubMed Abstract: 
  

Type IIA topoisomerases both manage the topological state of chromosomal DNA and are the targets of a variety of clinical agents. Bisdioxopiperazines are anticancer agents that associate with ATP-bound eukaryotic topoisomerase II (topo II) and convert the enzyme into an inactive, salt-stable clamp around DNA. To better understand both topo II and bisdioxopiperazine function, we determined the structures of the adenosine 5'-[beta,gamma-imino]-triphosphate-bound yeast topo II ATPase region (ScT2-ATPase) alone and complexed with the bisdioxopiperazine ICRF-187. The drug-free form of the protein is similar in overall fold to the equivalent region of bacterial gyrase but unexpectedly displays significant conformational differences. The ternary drug-bound complex reveals that ICRF-187 acts by an unusual mechanism of inhibition in which the drug does not compete for the ATP-binding pocket, but bridges and stabilizes a transient dimer interface between two ATPase protomers. Our data explain why bisdioxopiperazines target ATP-bound topo II, provide a structural rationale for the effects of certain drug-resistance mutations, and point to regions of bisdioxopiperazines that might be modified to improve or alter drug specificity.

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Organizational Affiliation: 

Department of Molecular and Cell Biology, 237 Hildebrand Hall, University of California, Berkeley, CA 94720-3206, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase II	A, B	418	Saccharomyces cerevisiae	Mutation(s): 10  Gene Names: TOP2 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P06786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P06786  Go to UniProtKB:  P06786

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	D [auth A], F [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.241 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.456	α = 90
b = 71.081	β = 90
c = 216.132	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-06-27 
• Released Date: 2003-08-26 
Deposition Author(s): Classen, S., Olland, S., Berger, J.M.

Revision History  

• Version 1.0: 2003-08-26
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description