4DDW

Thermotoga maritima reverse gyrase, c-centered orthorhombic form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1093/nar/gks1073
  • Primary Citation of Related Structures:  

  • 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 topois ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reverse gyrase
A
1104Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
Gene Names: rgy (topR)
Find proteins for O51934 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  O51934
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

Download SDF File 
Download CCD File 
A
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.209 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 174.325α = 90.00
b = 175.646β = 90.00
c = 104.135γ = 90.00
Software Package:
Software NamePurpose
SADABSdata scaling
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-02-06
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description