Thermotoga maritima reverse gyrase, C2 FORM 1

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.218 

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This is version 1.3 of the entry. See complete history


Crystal structures of Thermotoga maritima reverse gyrase: inferences for the mechanism of positive DNA supercoiling.

Rudolph, M.G.Del Toro Duany, Y.Jungblut, S.P.Ganguly, A.Klostermeier, D.

(2013) Nucleic Acids Res 41: 1058-1070

  • DOI: https://doi.org/10.1093/nar/gks1073
  • Primary Citation of Related Structures:  
    4DDT, 4DDU, 4DDV, 4DDW, 4DDX

  • PubMed Abstract: 

    Reverse gyrase is an ATP-dependent topoisomerase that is unique to hyperthermophilic archaea and eubacteria. The only reverse gyrase structure determined to date has revealed the arrangement of the N-terminal helicase domain and the C-terminal topoisomerase domain that intimately cooperate to generate the unique function of positive DNA supercoiling. Although the structure has elicited hypotheses as to how supercoiling may be achieved, it lacks structural elements important for supercoiling and the molecular mechanism of positive supercoiling is still not clear. We present five structures of authentic Thermotoga maritima reverse gyrase that reveal a first view of two interacting zinc fingers that are crucial for positive DNA supercoiling. The so-called latch domain, which connects the helicase and the topoisomerase domains is required for their functional cooperation and presents a novel fold. Structural comparison defines mobile regions in parts of the helicase domain, including a helical insert and the latch that are likely important for DNA binding during catalysis. We show that the latch, the helical insert and the zinc fingers contribute to the binding of DNA to reverse gyrase and are uniquely placed within the reverse gyrase structure to bind and guide DNA during strand passage. A possible mechanism for positive supercoiling by reverse gyrases is presented.

  • Organizational Affiliation

    pRED, Pharma Research and Early Development, Discovery Technologies, Grenzacherstrasse 124, CH-4070 Basel, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reverse gyrase1,104Thermotoga maritimaMutation(s): 0 
Gene Names: rgytopRTM_0173
EC: (PDB Primary Data), (PDB Primary Data)
Find proteins for O51934 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore O51934 
Go to UniProtKB:  O51934
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO51934
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.961α = 90
b = 73.912β = 116.59
c = 111.371γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SADABSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-02-06
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description