+
Open data
-
Basic information
Entry | Database: PDB / ID: 6f8h | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | antitoxin GraA | ||||||||||||
![]() | XRE family transcriptional regulator | ||||||||||||
![]() | ![]() ![]() | ||||||||||||
Function / homology | ![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Talavera, A. / Loris, R. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: A dual role in regulation and toxicity for the disordered N-terminus of the toxin GraT. Authors: Ariel Talavera / Hedvig Tamman / Andres Ainelo / Albert Konijnenberg / San Hadži / Frank Sobott / Abel Garcia-Pino / Rita Hõrak / Remy Loris / ![]() ![]() ![]() ![]() 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 ...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 GraTA 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. #1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017 Title: Production, biophysical characterization and crystallization of Pseudomonas putida GraA and its complexes with GraT and the graTA operator. Authors: Talavera, A. / Tamman, H. / Ainelo, A. / Hadaei, S. / Garcia-Pino, A. / Horak, R. / Konijnenberg, A. / Loris, R. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 88.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 67.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 11746.399 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.71 % / Description: needle |
---|---|
Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M KCl, 0.1 M HEPES pH 7.5, 15%(w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 90 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→46.81 Å / Num. obs: 27427 / % possible obs: 99.27 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.67 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.71 / Num. unique obs: 2703 / CC1/2: 0.97 / % possible all: 98.11 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.002→46.806 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|