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- PDB-5cze: Crystal structure of the PaaA2-ParE2 antitoxin-toxin complex -

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Basic information

Entry
Database: PDB / ID: 5cze
TitleCrystal structure of the PaaA2-ParE2 antitoxin-toxin complex
Components
  • PaaA2
  • Plasmid stabilization protein ParE
KeywordsTOXIN / toxin-antitoxin
Function / homologyParE toxin of type II toxin-antitoxin system, parDE / RelE-like / Toxin-antitoxin system, RelE/ParE toxin family / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / 2-Layer Sandwich / Alpha Beta / Plasmid stabilization protein ParE / :
Function and homology information
Biological speciesEscherichia coli O157:H7 str. SS52 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.82 Å
AuthorsLoris, R. / Sterckx, Y.G.J.
CitationJournal: J Mol Biol / Year: 2016
Title: A unique hetero-hexadecameric architecture displayed by the Escherichia coli O157 PaaA2-ParE2 antitoxin-toxin complex.
Authors: Yann G-J Sterckx / Thomas Jové / Alexander V Shkumatov / Abel Garcia-Pino / Lieselotte Geerts / Maia De Kerpel / Jurij Lah / Henri De Greve / Laurence Van Melderen / Remy Loris /
Abstract: Many bacterial pathogens modulate their metabolic activity, virulence and pathogenicity through so-called "toxin-antitoxin" (TA) modules. The genome of the human pathogen Escherichia coli O157 ...Many bacterial pathogens modulate their metabolic activity, virulence and pathogenicity through so-called "toxin-antitoxin" (TA) modules. The genome of the human pathogen Escherichia coli O157 contains two three-component TA modules related to the known parDE module. Here, we show that the toxin EcParE2 maps in a branch of the RelE/ParE toxin superfamily that is distinct from the branches that contain verified gyrase and ribosome inhibitors. The structure of EcParE2 closely resembles that of Caulobacter crescentus ParE but shows a distinct pattern of conserved surface residues, in agreement with its apparent inability to interact with GyrA. The antitoxin EcPaaA2 is characterized by two α-helices (H1 and H2) that serve as molecular recognition elements to wrap itself around EcParE2. Both EcPaaA2 H1 and H2 are required to sustain a high-affinity interaction with EcParE2 and for the inhibition of EcParE2-mediated killing in vivo. Furthermore, evidence demonstrates that EcPaaA2 H2, but not H1, determines specificity for EcParE2. The initially formed EcPaaA2-EcParE2 heterodimer then assembles into a hetero-hexadecamer, which is stable in solution and is formed in a highly cooperative manner. Together these findings provide novel data on quaternary structure, TA interactions and activity of a hitherto poorly characterized family of TA modules.
History
DepositionJul 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PaaA2
B: Plasmid stabilization protein ParE
C: PaaA2
D: Plasmid stabilization protein ParE
I: PaaA2
J: Plasmid stabilization protein ParE
K: PaaA2
L: Plasmid stabilization protein ParE


Theoretical massNumber of molelcules
Total (without water)81,8098
Polymers81,8098
Non-polymers00
Water0
1
A: PaaA2
B: Plasmid stabilization protein ParE
C: PaaA2
D: Plasmid stabilization protein ParE
I: PaaA2
J: Plasmid stabilization protein ParE
K: PaaA2
L: Plasmid stabilization protein ParE

A: PaaA2
B: Plasmid stabilization protein ParE
C: PaaA2
D: Plasmid stabilization protein ParE
I: PaaA2
J: Plasmid stabilization protein ParE
K: PaaA2
L: Plasmid stabilization protein ParE


Theoretical massNumber of molelcules
Total (without water)163,61816
Polymers163,61816
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area44730 Å2
ΔGint-216 kcal/mol
Surface area50830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.226, 143.226, 86.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
PaaA2


Mass: 8661.044 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 str. SS52 (bacteria)
Gene: SS52_2228 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F6F6Q9
#2: Protein
Plasmid stabilization protein ParE / Plasmid stabilization system protein


Mass: 11791.259 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 str. SS52 (bacteria)
Gene: relE2, AML07_29260, APZ14_24120, ARC77_01680, ERS085383_05243, ERS085404_05085, ERS150873_04952, JEONG1266_09605
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D7C2L1

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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: 3.17 Å3/Da / Density % sol: 61.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 20 mM calcium chloride, 100 mM sodium acetate pH 4.6, 30% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 3.822→46.88 Å / Num. obs: 9903 / % possible obs: 97.1 % / Redundancy: 7.8 % / Biso Wilson estimate: 124.93 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 12.91
Reflection shellResolution: 3.82→3.96 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 3.1 / Num. unique all: 841 / % possible all: 83.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CW7

5cw7


Resolution: 3.82→46.88 Å / Cor.coef. Fo:Fc: 0.805 / Cor.coef. Fo:Fc free: 0.796 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.813
RfactorNum. reflection% reflectionSelection details
Rfree0.306 496 5.01 %RANDOM
Rwork0.253 ---
obs0.256 9903 97 %-
Displacement parametersBiso mean: 113.38 Å2
Baniso -1Baniso -2Baniso -3
1-12.3554 Å20 Å20 Å2
2--12.3554 Å20 Å2
3----24.7108 Å2
Refine analyzeLuzzati coordinate error obs: 0.61 Å
Refinement stepCycle: LAST / Resolution: 3.82→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4993 0 0 0 4993
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015125HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.146987HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1755SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes116HARMONIC2
X-RAY DIFFRACTIONt_gen_planes746HARMONIC5
X-RAY DIFFRACTIONt_it5125HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.62
X-RAY DIFFRACTIONt_other_torsion21.72
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion670SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6054SEMIHARMONIC4
LS refinement shellResolution: 3.82→4.27 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.317 133 5 %
Rwork0.285 2529 -
all0.286 2662 -
obs--93.46 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-1.283-0.6882-3.97576.23291.06530-0.40690.20730.7435-0.320.1733-0.1992-0.09630.06410.23360.34450.08180.2013-0.101-0.04480.3048.352671.4619-10.1652
20.69032.2404-3.97574.82461.06533.13970.0687-0.33240.41340.0344-0.4284-0.05390.19030.140.35960.2327-0.04240.1924-0.0693-0.02930.30412.721365.9977-10.0773
3-1.6990.0324-3.97574.98491.06530-0.21170.03120.57180.50240.19310.09820.2984-0.34190.01860.164-0.2328-0.05560.0818-0.20760.30415.576664.175915.2827
45.13851.0762-3.784510.61711.17570-0.08770.68960.7435-0.0376-0.0469-0.1992-0.3188-0.34650.13450.1457-0.06190.1041-0.1338-0.11540.30415.000659.723310.8482
50.6210.5761-2.74175.4604-1.0723.54830.5146-0.25750.3272-0.2575-0.44480.0318-0.4016-0.3929-0.06980.3140.13470.0728-0.19250.17780.1133-8.480336.3641-6.338
61.9950.2905-3.5254.49880.28471.82420.1583-0.12370.1951-0.29950.3351-0.0081-0.1721-0.1897-0.49340.32470.11610.1662-0.16030.0160.0207-2.763138.8601-4.9836
72.0306-0.7347-0.0424-1.5252-1.347500.4233-0.3194-0.5372-0.21240.0270.2286-0.49120.1535-0.45030.3621-0.05590.20760.0757-0.05560.12161.58427.305317.0312
84.45073.9827-2.18526.11341.38811.13540.5193-0.4444-0.4011-0.2284-0.0998-0.104-0.4429-0.0562-0.41950.2884-0.0890.09040.0402-0.1233-0.14316.378529.152512.7517
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ I|* }
6X-RAY DIFFRACTION6{ J|* }
7X-RAY DIFFRACTION7{ K|* }
8X-RAY DIFFRACTION8{ L|* }

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