2ZBK

Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer mechanisms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.56 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.312 
  • R-Value Observed: 0.313 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of an Intact Type II DNA Topoisomerase: Insights into DNA Transfer Mechanisms

Graille, M.Durand, D.Lecointe, F.Gadelle, D.Quevillon-Cheruel, S.Vachette, P.Forterre, P.van Tilbeurgh, H.

(2008) Structure 16: 360-370

  • DOI: 10.1016/j.str.2007.12.020
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • DNA topoisomerases resolve DNA topological problems created during transcription, replication, and recombination. These ubiquitous enzymes are essential for cell viability and are highly potent targets for the development of antibacterial and antitum ...

    DNA topoisomerases resolve DNA topological problems created during transcription, replication, and recombination. These ubiquitous enzymes are essential for cell viability and are highly potent targets for the development of antibacterial and antitumoral drugs. Type II enzymes catalyze the transfer of a DNA duplex through another one in an ATP-dependent mechanism. Because of its small size and sensitivity to antitumoral drugs, the archaeal DNA topoisomerase VI, a type II enzyme, is an excellent model for gaining further understanding of the organization and mechanism of these enzymes. We present the crystal structure of intact DNA topoisomerase VI bound to radicicol, an inhibitor of human topo II, and compare it to the conformation of the apo-protein as determined by small-angle X-ray scattering in solution. This structure, combined with a wealth of experimental data gathered on these enzymes, allows us to propose a structural model for the two-gate DNA transfer mechanism.


    Organizational Affiliation

    Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR8619 CNRS, Université Paris-Sud, IFR115, F-91405 Orsay, France.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Type II DNA topoisomerase VI subunit AA, C, E, G389Saccharolobus shibataeMutation(s): 0 
Gene Names: top6A
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
Find proteins for O05208 (Saccharolobus shibatae)
Explore O05208 
Go to UniProtKB:  O05208
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Type 2 DNA topoisomerase 6 subunit BB, D, F, H530Saccharolobus shibataeMutation(s): 0 
Gene Names: top6B
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
Find proteins for O05207 (Saccharolobus shibatae)
Explore O05207 
Go to UniProtKB:  O05207
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RDC
Query on RDC

Download CCD File 
B, D, F, H
RADICICOL
C18 H17 Cl O6
WYZWZEOGROVVHK-GTMNPGAYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RDCKd :  2000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.56 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.312 
  • R-Value Observed: 0.313 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.96α = 90
b = 200.53β = 90
c = 329.07γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
SHELXDphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance