2Q2E

Crystal structure of the topoisomerase VI holoenzyme from Methanosarcina mazei


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.349 
  • R-Value Work: 0.306 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/nsmb1264

  • 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 V ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Type II DNA topoisomerase VI subunit A
A
369Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)Mutation(s): 0 
Gene Names: top6A
EC: 5.99.1.3
Find proteins for Q8PUB7 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88))
Go to UniProtKB:  Q8PUB7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Type 2 DNA topoisomerase 6 subunit B
B
621Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)Mutation(s): 0 
Gene Names: top6B
EC: 5.99.1.3
Find proteins for Q8PUB8 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88))
Go to UniProtKB:  Q8PUB8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.349 
  • R-Value Work: 0.306 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 227.812α = 90.00
b = 227.812β = 90.00
c = 208.660γ = 120.00
Software Package:
Software NamePurpose
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance