2Q2E

Crystal structure of the topoisomerase VI holoenzyme from Methanosarcina mazei


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.349 
  • R-Value Work: 0.306 
  • R-Value Observed: 0.308 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Holoenzyme assembly and ATP-mediated conformational dynamics of topoisomerase VI

Corbett, K.D.Benedetti, P.Berger, J.M.

(2007) Nat Struct Mol Biol 14: 611-619

  • DOI: https://doi.org/10.1038/nsmb1264
  • Primary Citation of Related Structures:  
    2Q2E

  • PubMed Abstract: 

    Type II topoisomerases help disentangle chromosomes to facilitate cell division. To advance understanding of the structure and dynamics of these essential enzymes, we have determined the crystal structure of an archaeal type IIB topoisomerase, topo VI, at 4.0-A resolution. The 220-kDa heterotetramer adopts a 'twin-gate' architecture, in which a pair of ATPase domains at one end of the enzyme is poised to coordinate DNA movements into the enzyme and through a set of DNA-cleaving domains at the other end. Small-angle X-ray scattering studies show that nucleotide binding elicits a major structural reorganization that is propagated to the enzyme's DNA-cleavage center, explaining how ATP is coupled to DNA capture and strand scission. These data afford important insights into the mechanisms of topo VI and related proteins, including type IIA topoisomerases and the Spo11 meiotic recombination endonuclease.


  • Organizational Affiliation

    Department of Molecular and Cellular Biology, QB3 Institute, Stanley Hall #3220, University of California, Berkeley, California 94720-3220, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Type II DNA topoisomerase VI subunit A369Methanosarcina mazeiMutation(s): 0 
Gene Names: top6A
EC: 5.99.1.3
UniProt
Find proteins for Q8PUB7 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88))
Explore Q8PUB7 
Go to UniProtKB:  Q8PUB7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8PUB7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Type 2 DNA topoisomerase 6 subunit B621Methanosarcina mazeiMutation(s): 0 
Gene Names: top6B
EC: 5.99.1.3
UniProt
Find proteins for Q8PUB8 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88))
Explore Q8PUB8 
Go to UniProtKB:  Q8PUB8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8PUB8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.349 
  • R-Value Work: 0.306 
  • R-Value Observed: 0.308 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 227.812α = 90
b = 227.812β = 90
c = 208.66γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references