6F8S

Toxin-Antitoxin complex GraTA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

  • DOI: 10.1038/s41467-019-08865-z
  • Primary Citation of 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 ...

    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.

    Related Citations: 
    • Production, biophysical characterization and crystallization of Pseudomonas putida GraA and its complexes with GraT and the graTA operator.
      Talavera, A., Tamman, H., Ainelo, A., Hadaei, S., Garcia-Pino, A., Horak, R., Konijnenberg, A., Loris, R.
      (2017) Acta Crystallogr F Struct Biol Commun 73: 455
    Organizational Affiliation: 

    Molecular Recognition Unit, Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, B-1050, Brussel, Belgium. remy.loris@vub.be.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
XRE family transcriptional regulatorA, C99Pseudomonas putidaMutation(s): 0 
Gene Names: AYO08_18510
UniProt
Find proteins for Q88MI6 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440))
Explore Q88MI6 
Go to UniProtKB:  Q88MI6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ88MI6
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Putative Killer proteinB, D98Pseudomonas putida KT2440Mutation(s): 0 
Gene Names: PP_1586
UniProt
Find proteins for Q88MI5 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440))
Explore Q88MI5 
Go to UniProtKB:  Q88MI5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ88MI5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG
Download Ideal Coordinates CCD File 
F [auth B],
H [auth D],
I [auth D]		DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
E [auth A],
G [auth C]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.03α = 90
b = 56.03β = 90
c = 128.19γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Fonds voor Wetenschappelijk Onderzoek VlaanderenBelgiumG.0135.15N, GOC1213N, G.0090.11N
Vrije Universiteit BrusselBelgiumOZR2232 to SH, SPR13
BioStruct-XBelgium1673, 6131

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-09-12
    Changes: Data collection, Database references
  • Version 1.2: 2019-03-13
    Changes: Data collection, Database references