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- PDB-6f8h: antitoxin GraA -

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Basic information

Entry
Database: PDB / ID: 6f8h
Titleantitoxin GraA
ComponentsXRE family transcriptional regulator
KeywordsANTITOXIN / GraA / HigA
Function / homology
Function and homology information


Toxin-antitoxin system, antidote protein, HigA / 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
XRE family transcriptional regulator
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 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 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 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 1.2May 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: XRE family transcriptional regulator
C: XRE family transcriptional regulator
D: XRE family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)46,9864
Polymers46,9864
Non-polymers00
Water4,342241
1
A: XRE family transcriptional regulator

D: XRE family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)23,4932
Polymers23,4932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y+1/2,-z+11
Buried area2960 Å2
ΔGint-23 kcal/mol
Surface area10150 Å2
MethodPISA
2
B: XRE family transcriptional regulator

C: XRE family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)23,4932
Polymers23,4932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_857-x+3,y+1/2,-z+21
Buried area2790 Å2
ΔGint-25 kcal/mol
Surface area9570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.740, 48.950, 66.930
Angle α, β, γ (deg.)90.00, 92.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
XRE family transcriptional regulator


Mass: 11746.399 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: AYO08_18510 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A179R2V1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.19 Å3/Da / Density % sol: 43.71 % / Description: needle
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M KCl, 0.1 M HEPES pH 7.5, 15%(w/v) PEG 6000

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.002→46.806 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 25.12
RfactorNum. reflection% reflection
Rfree0.2258 2537 4.95 %
Rwork0.19 --
obs0.1918 27427 95.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.002→46.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2877 0 0 241 3118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012921
X-RAY DIFFRACTIONf_angle_d1.1243956
X-RAY DIFFRACTIONf_dihedral_angle_d13.2171078
X-RAY DIFFRACTIONf_chiral_restr0.05458
X-RAY DIFFRACTIONf_plane_restr0.006525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.002-2.04050.31461430.25532672X-RAY DIFFRACTION92
2.0405-2.08220.34981380.25682714X-RAY DIFFRACTION97
2.0822-2.12750.23391410.22932720X-RAY DIFFRACTION96
2.1275-2.17690.30931410.23222713X-RAY DIFFRACTION97
2.1769-2.23140.31311460.25222716X-RAY DIFFRACTION95
2.2314-2.29170.39841280.33842530X-RAY DIFFRACTION91
2.2917-2.35910.29451390.21612707X-RAY DIFFRACTION96
2.3591-2.43530.23461420.20162770X-RAY DIFFRACTION97
2.4353-2.52230.29851420.20452737X-RAY DIFFRACTION97
2.5223-2.62330.26271440.20022738X-RAY DIFFRACTION97
2.6233-2.74270.22441470.20512774X-RAY DIFFRACTION97
2.7427-2.88730.27761420.2162754X-RAY DIFFRACTION98
2.8873-3.06810.26361440.21122747X-RAY DIFFRACTION97
3.0681-3.3050.28941410.20522754X-RAY DIFFRACTION97
3.305-3.63740.17091400.18362662X-RAY DIFFRACTION95
3.6374-4.16350.17151370.1492674X-RAY DIFFRACTION94
4.1635-5.24450.16861410.1442666X-RAY DIFFRACTION94
5.2445-46.81840.16371410.152692X-RAY DIFFRACTION95

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