4GFH

Topoisomerase II-DNA-AMPPNP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.408 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of a topoisomerase II-DNA-nucleotide complex reveals a new control mechanism for ATPase activity.

Schmidt, B.H.Osheroff, N.Berger, J.M.

(2012) Nat.Struct.Mol.Biol. 19: 1147-1154

  • DOI: 10.1038/nsmb.2388

  • PubMed Abstract: 
  • Type IIA topoisomerases control DNA supercoiling and disentangle chromosomes through a complex ATP-dependent strand-passage mechanism. Although a general framework exists for type IIA topoisomerase function, the architecture of the full-length enzyme ...

    Type IIA topoisomerases control DNA supercoiling and disentangle chromosomes through a complex ATP-dependent strand-passage mechanism. Although a general framework exists for type IIA topoisomerase function, the architecture of the full-length enzyme has remained undefined. Here we present the structure of a fully catalytic Saccharomyces cerevisiae topoisomerase II homodimer complexed with DNA and a nonhydrolyzable ATP analog. The enzyme adopts a domain-swapped configuration wherein the ATPase domain of one protomer sits atop the nucleolytic region of its partner subunit. This organization produces an unexpected interaction between bound DNA and a conformational transducing element in the ATPase domain, which we show is critical for both DNA-stimulated ATP hydrolysis and global topoisomerase activity. Our data indicate that the ATPase domains pivot about each other to ensure unidirectional strand passage and that this state senses bound DNA to promote ATP turnover and enzyme reset.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA topoisomerase 2
A, F
1177Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TOP2 (TOR3)
EC: 5.99.1.3
Find proteins for P06786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P06786
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3')B,G11N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)-3')C,H15N/A
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*(TSP))-3')D,I11N/A
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)-3')E,J15N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, F
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
TSP
Query on TSP
D, I
NON-POLYMERC10 H15 N2 O7 P ST
PTR
Query on PTR
A, F
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.408 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 169.135α = 90.00
b = 169.884β = 90.00
c = 169.212γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2012-12-12
    Type: Database references