9IMJ | pdb_00009imj

Bacteriophage T6 topoisomerase II ATPase domain crystal strcuture


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.289 (Depositor), 0.291 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

Starting Model: in silico
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Literature

Structural and functional insights into the T-even type bacteriophage topoisomerase II.

Xin, Y.Xian, R.Yang, Y.Cong, J.Rao, Z.Li, X.Chen, Y.

(2024) Nat Commun 15: 8719-8719

  • DOI: https://doi.org/10.1038/s41467-024-53037-3
  • Primary Citation of Related Structures:  
    8YLU, 8YO1, 8YO3, 8YO4, 8YO5, 8YO7, 8YO9, 8YOD, 8YON, 9IMJ

  • PubMed Abstract: 

    T-even type bacteriophages are virulent phages commonly used as model organisms, playing a crucial role in understanding various biological processes. One such process involves the regulation of DNA topology during phage replication upon host infection, governed by type IIA DNA topoisomerases. In spite of various studies on prokaryotic and eukaryotic counterparts, viral topoisomerase II remains insufficiently understood, especially the unique domain composition of T4 phage. In this study, we determine the cryo-EM structures of topoisomerase II from T4 and T6 phages, including full-length structures of both apo and DNA-binding states which have never been determined before. Together with other conformational states, these structures provide an explicit blueprint of mechanisms of phage topoisomerase II. Particularly, the asymmetric dimeric interactions observed in cryo-EM structures of T6 phage topoisomerase II ATPase domain and central domain bound with DNA shed light on the asynchronous ATP usage and asynchronous cleavage of the G-segment DNA, respectively. The elucidation of phage topoisomerase II's structures and functions not only enhances our understanding of mechanisms and evolutionary parallels with prokaryotic and eukaryotic homologs but also highlights its potential as a model for developing type IIA topoisomerase inhibitors.


  • Organizational Affiliation
    • National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA topoisomerase (ATP-hydrolyzing)386Enterobacteria phage T6Mutation(s): 0 
Gene Names: EcT6_00003
EC: 5.6.2.2
UniProt
Find proteins for A0A346FJ89 (Enterobacteria phage T6)
Explore A0A346FJ89 
Go to UniProtKB:  A0A346FJ89
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A346FJ89
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.289 (Depositor), 0.291 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.989α = 90
b = 90.989β = 90
c = 102.9γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-25
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Database references, Structure summary