Structure of Full Length Topoisomerase I from Thermotoga maritima in triclinic crystal form

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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Crystal Structure of Full Length Topoisomerase I from Thermotoga maritima

Hansen, G.Harrenga, A.Wieland, B.Schomburg, D.Reinemer, P.

(2006) J Mol Biol 358: 1328-1340

  • DOI: https://doi.org/10.1016/j.jmb.2006.03.012
  • Primary Citation of Related Structures:  
    2GAI, 2GAJ

  • PubMed Abstract: 

    DNA topoisomerases are a family of enzymes altering the topology of DNA by concerted breakage and rejoining of the phosphodiester backbone of DNA. Bacterial and archeal type IA topoisomerases, including topoisomerase I, topoisomerase III, and reverse gyrase, are crucial in regulation of DNA supercoiling and maintenance of genetic stability. The crystal structure of full length topoisomerase I from Thermotoga maritima was determined at 1.7A resolution and represents an intact and fully active bacterial topoisomerase I. It reveals the torus-like structure of the conserved transesterification core domain comprising domains I-IV and a tightly associated C-terminal zinc ribbon domain (domain V) packing against domain IV of the core domain. The previously established zinc-independence of the functional activity of T.maritima topoisomerase I is further supported by its crystal structure as no zinc ion is bound to domain V. However, the structural integrity is preserved by the formation of two disulfide bridges between the four Zn-binding cysteine residues. A functional role of domain V in DNA binding and recognition is suggested and discussed in the light of the structure and previous biochemical findings. In addition, implications for bacterial topoisomerases I are provided.

  • Organizational Affiliation

    Bayer HealthCare AG, Pharma R and D Europe, Enabling Technologies, D-42096 Wuppertal, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA topoisomerase I
A, B
633Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: topATM_0258
EC: (PDB Primary Data), (UniProt)
Find proteins for P46799 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore P46799 
Go to UniProtKB:  P46799
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46799
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.118α = 83.4
b = 95.421β = 86.15
c = 96.508γ = 84.87
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2006-04-25 
  • Deposition Author(s): Hansen, G.

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-25
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Refinement description