2Q2E | pdb_00002q2e

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 (Depositor), 0.283 (DCC) 
  • R-Value Work: 
    0.306 (Depositor), 0.301 (DCC) 
  • R-Value Observed: 
    0.308 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2Q2E

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 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.

Macromolecule Content 

  • Total Structure Weight: 111.03 kDa 
  • Atom Count: 7,039 
  • Modeled Residue Count: 897 
  • Deposited Residue Count: 990 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  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 (PDB Primary Data), 5.6.2.2 (UniProt)
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:|  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 (PDB Primary Data), 5.6.2.2 (UniProt)
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 (Depositor), 0.283 (DCC) 
  • R-Value Work:  0.306 (Depositor), 0.301 (DCC) 
  • R-Value Observed: 0.308 (Depositor) 
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

View Full Validation Report



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