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- PDB-6f8s: Toxin-Antitoxin complex GraTA -

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Basic information

Entry
Database: PDB / ID: 6f8s
TitleToxin-Antitoxin complex GraTA
Components
  • Putative Killer protein
  • XRE family transcriptional regulator
KeywordsTOXIN / GraA / GraT / HigA / HigB / GraTA / HigBA
Function / homology
Function and homology information


molecular function activator activity / DNA binding
Similarity search - Function
Toxin HigB-1 / RelE-like toxin of type II toxin-antitoxin system HigB / Toxin-antitoxin system, antidote protein, HigA / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) ...Toxin HigB-1 / RelE-like toxin of type II toxin-antitoxin system HigB / Toxin-antitoxin system, antidote protein, HigA / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / XRE family transcriptional regulator / Killer protein / Antidote protein
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTalavera, A. / Loris, R.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Fonds voor Wetenschappelijk Onderzoek VlaanderenG.0135.15N, GOC1213N, G.0090.11N Belgium
Vrije Universiteit BrusselOZR2232 to SH, SPR13 Belgium
BioStruct-X1673, 6131 Belgium
Citation
Journal: Nat Commun / Year: 2019
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
DepositionDec 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: XRE family transcriptional regulator
B: Putative Killer protein
C: XRE family transcriptional regulator
D: Putative Killer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9299
Polymers44,4184
Non-polymers5105
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-59 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.030, 56.030, 128.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein XRE family transcriptional regulator


Mass: 10917.521 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: antitoxin GraA / Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: AYO08_18510 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A179R2V1, UniProt: Q88MI6*PLUS
#2: Protein Putative Killer protein


Mass: 11291.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: toxin GraT
Source: (gene. exp.) Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440) (bacteria)
Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: PP_1586 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q88MI5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.8 M Li 2 SO 4 , 0.1 M sodium acetate trihydrate pH 4.0, 4%(v/v) PEG 200

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.5→42.18 Å / Num. obs: 13706 / % possible obs: 99.87 % / Redundancy: 9.8 % / Biso Wilson estimate: 66.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08967 / Rrim(I) all: 0.0946 / Net I/σ(I): 16.82
Reflection shellResolution: 2.5→2.587 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.866 / Num. unique obs: 1354 / CC1/2: 0.82 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→42.18 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.23 / Phase error: 24.77
RfactorNum. reflection% reflection
Rfree0.2115 1349 5.01 %
Rwork0.1782 --
obs0.1799 26952 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→42.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2455 0 31 11 2497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092520
X-RAY DIFFRACTIONf_angle_d1.1783408
X-RAY DIFFRACTIONf_dihedral_angle_d14.534922
X-RAY DIFFRACTIONf_chiral_restr0.042391
X-RAY DIFFRACTIONf_plane_restr0.005444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.58950.29591320.27332553X-RAY DIFFRACTION99
2.5895-2.69320.29891350.25392586X-RAY DIFFRACTION100
2.6932-2.81570.27431340.2522561X-RAY DIFFRACTION100
2.8157-2.96410.30231350.24482559X-RAY DIFFRACTION100
2.9641-3.14980.291380.22072570X-RAY DIFFRACTION100
3.1498-3.39290.23431340.19952544X-RAY DIFFRACTION100
3.3929-3.73410.17811350.17252575X-RAY DIFFRACTION100
3.7341-4.2740.19011340.142564X-RAY DIFFRACTION100
4.274-5.3830.16261340.14662545X-RAY DIFFRACTION100
5.383-42.19020.20131380.16662546X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 76.2375 Å / Origin y: 7.6023 Å / Origin z: 63.9458 Å
111213212223313233
T0.3815 Å20.0767 Å2-0.0408 Å2-0.3799 Å2-0.0371 Å2--0.4253 Å2
L0.7647 °20.6424 °2-0.1573 °2-0.8968 °2-0.0549 °2--1.9894 °2
S-0.0418 Å °0.0817 Å °-0.0343 Å °0.0654 Å °-0.0028 Å °-0.0421 Å °0.0211 Å °-0.0233 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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