6FIX | pdb_00006fix

antitoxin GraA in complex with its operator

• PDB DOI: https://doi.org/10.2210/pdb6FIX/pdb
• NAKB: 6FIX

• Classification: ANTITOXIN
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-19 Released: 2019-01-30 
• Deposition Author(s): Talavera, A., Loris, R.
• Funding Organization(s): Fonds voor Wetenschappelijk Onderzoek Vlaanderen, Vrije Universiteit Brussel, BioStruct-X

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 
  0.286 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.256 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Literature

A dual role in regulation and toxicity for the disordered N-terminus of the toxin GraT.

Talavera, A., Tamman, H., Ainelo, A., Konijnenberg, A., Hadzi, S., Sobott, F., Garcia-Pino, A., Horak, R., Loris, R.

(2019) Nat Commun 10: 972-972

• PubMed: 30814507 
• DOI: https://doi.org/10.1038/s41467-019-08865-z
• Primary Citation Related Structures: 
  6F8H, 6F8S, 6FIX


• PubMed Abstract: 
  

  Bacterial toxin-antitoxin (TA) modules are tightly regulated to maintain growth in favorable conditions or growth arrest during stress. A typical regulatory strategy involves the antitoxin binding and repressing its own promoter while the toxin often acts as a co-repressor. Here we show that Pseudomonas putida graTA-encoded antitoxin GraA and toxin GraT differ from other TA proteins in the sense that not the antitoxin but the toxin possesses a flexible region. GraA auto-represses the graTA promoter: two GraA dimers bind cooperatively at opposite sides of the operator sequence. Contrary to other TA modules, GraT is a de-repressor of the graTA promoter as its N-terminal disordered segment prevents the binding of the GraT ₂ A ₂ complex to the operator. Removal of this region restores operator binding and abrogates Gr aT toxicity. GraTA represents a TA module where a flexible region in the toxin rather than in the antitoxin controls operon expression and toxin activity.

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Organizational Affiliation: 
• Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050, Brussel, Belgium. [e-mail].
Molecular Recognition Unit, Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, B-1050, Brussel, Belgium. [e-mail].
Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia.
Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050, Brussel, Belgium.
Molecular Recognition Unit, Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, B-1050, Brussel, Belgium.
Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020, Antwerpen, Belgium.
Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia.
Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
Biologie Structurale et Biophysique, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, B-6041, Gosselies, Belgium.
Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050, Brussel, Belgium. [e-mail].
Molecular Recognition Unit, Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, B-1050, Brussel, Belgium. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 65.72 kDa 
• Atom Count: 4,036 
• Modeled Residue Count: 441 
• Deposited Residue Count: 481 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
XRE family transcriptional regulator	A, B, D, E	105	Pseudomonas putida	Mutation(s): 0  Gene Names: AYO08_18510

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (30-MER)	C	31	Pseudomonas putida

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (30-MER)	F	30	Pseudomonas putida

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free:  0.286 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.256 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.55	α = 90
b = 105.55	β = 90
c = 149.94	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-30 
Deposition Author(s): Talavera, A., Loris, R.

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Funding Organization	Location	Grant Number
Fonds voor Wetenschappelijk Onderzoek Vlaanderen	Belgium	G.0135.15N, GOC1213N, G.0090.11N
Vrije Universiteit Brussel	Belgium	OZR2232 to SH, SPR13
BioStruct-X	Belgium	1673, 6131

Revision History  

• Version 1.0: 2019-01-30
  Type: Initial release
  
• Version 2.0: 2019-02-06
  Changes: Data collection, Derived calculations, Polymer sequence, Structure summary
• Version 2.1: 2019-03-13
  Changes: Data collection, Database references
• Version 2.2: 2024-05-08
  Changes: Advisory, Data collection, Database references