Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 128.67 kDa 
• Atom Count: 9033 
• Modelled Residue Count: 1102 
• Deposited Residue Count: 1104 
• Unique protein chains: 1

4DDU

Thermotoga maritima reverse gyrase, C2 FORM 1

• DOI: 10.2210/pdb4DDU/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-19 Released: 2012-12-26 
• Deposition Author(s): Rudolph, M.G., Klostermeier, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.278 
• R-Value Work: 0.214 
• R-Value Observed: 0.218 

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

• PubMed: 23209025 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse gyrase	A	1104	Thermotoga maritima	Mutation(s): 0  Gene Names: rgy, topR, TM_0173 EC: 3.6.4.12 (PDB Primary Data), 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for O51934 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)) Explore O51934  Go to UniProtKB:  O51934

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 169.961	α = 90
b = 73.912	β = 116.59
c = 111.371	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SADABS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-19 
• Released Date: 2012-12-26 
Deposition Author(s): Rudolph, M.G., Klostermeier, D.

Revision History  

• 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