Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 111032.66 
• Atom Count: 7039 
• Residue Count: 990 
• Unique protein chains: 2

2Q2E

Crystal structure of the topoisomerase VI holoenzyme from Methanosarcina mazei

• DOI: 10.2210/pdb2Q2E/pdb

• Classification: ISOMERASE
• Organism(s): Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)
• Expression System: Escherichia coli


• Deposited: 2007-05-28 Released: 2007-07-10 
• Deposition Author(s): Corbett, K.D., Benedetti, P., Berger, J.M.

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Experimental Data Snapshot

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

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

• PubMed: 17603498 
• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
Type II DNA topoisomerase VI subunit A	A	369	Methanosarcina 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
Molecule	Chains	Sequence Length	Organism	Details
Type 2 DNA topoisomerase 6 subunit B	B	621	Methanosarcina 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 = 227.812	α = 90.00
b = 227.812	β = 90.00
c = 208.660	γ = 120.00

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOSFLM	data reduction
SCALA	data scaling
MLPHARE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-05-28 
• Released Date: 2007-07-10 
• Deposition Author(s): Corbett, K.D., Benedetti, P., Berger, J.M.

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