6Z03

DNA Topoisomerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Topoisomerase I (TOP1) dynamics: conformational transition from open to closed states.

Takahashi, D.T.Gadelle, D.Agama, K.Kiselev, E.Zhang, H.Yab, E.Petrella, S.Forterre, P.Pommier, Y.Mayer, C.

(2022) Nat Commun 13: 59-59

  • DOI: https://doi.org/10.1038/s41467-021-27686-7
  • Primary Citation of Related Structures:  
    6Z01, 6Z03

  • PubMed Abstract: 

    Eukaryotic topoisomerases I (TOP1) are ubiquitous enzymes removing DNA torsional stress. However, there is little data concerning the three-dimensional structure of TOP1 in the absence of DNA, nor how the DNA molecule can enter/exit its closed conformation. Here, we solved the structure of thermostable archaeal Caldiarchaeum subterraneum CsTOP1 in an apo-form. The enzyme displays an open conformation resulting from one substantial rotation between the capping (CAP) and the catalytic (CAT) modules. The junction between these two modules is a five-residue loop, the hinge, whose flexibility permits the opening/closing of the enzyme and the entry of DNA. We identified a highly conserved tyrosine near the hinge as mediating the transition from the open to closed conformation upon DNA binding. Directed mutagenesis confirmed the importance of the hinge flexibility, and linked the enzyme dynamics with sensitivity to camptothecin, a TOP1 inhibitor targeting the TOP1 enzyme catalytic site in the closed conformation.


  • Organizational Affiliation

    Institut de Biologie Integrative de la Cellule, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, Cedex, France. dtakahashi@unistra.fr.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA topoisomerase I
A, B
539Candidatus Caldarchaeum subterraneumMutation(s): 0 
Gene Names: HGMM_F15C04C08
EC: 5.99.1.2
UniProt
Find proteins for E6N697 (Caldiarchaeum subterraneum)
Explore E6N697 
Go to UniProtKB:  E6N697
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE6N697
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.47α = 90
b = 94.68β = 111.81
c = 92.65γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
autoPROCdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-17-CE12-0032

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-17
    Type: Initial release
  • Version 1.1: 2023-05-31
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description