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- SASDC84: parDE-like toxin-antitoxin module, EcPaaA2_13-63-HisEcParE2 construct -

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Open data


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Basic information

Entry
Database: SASBDB / ID: SASDC84
SampleparDE-like toxin-antitoxin module, EcPaaA2_13-63-HisEcParE2 construct
  • Plasmid stabilization protein ParE (protein), ParE2, Escherichia coli
  • Uncharacterized protein (protein), PaaA2, Escherichia coli O157:H7 str. SS52
Function / homology: / ParE toxin of type II toxin-antitoxin system, parDE / Toxin-antitoxin system, RelE/ParE toxin family / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Plasmid stabilization protein ParE / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
Escherichia coli O157:H7 str. SS52 (bacteria)
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.
Contact author
  • Alexander Shkumatov (VUB, Vrije Universiteit Brussel, Pleinlaan 2 1050 Brussel)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Models

Model #1318
Type: atomic / Software: (r4556/NA) / Radius of dummy atoms: 1.90 A / Chi-square value: 0.760
Search similar-shape structures of this assembly by Omokage search (details)
Model #1319
Type: atomic / Software: (r4556/NA) / Radius of dummy atoms: 1.90 A / Chi-square value: 0.760
Search similar-shape structures of this assembly by Omokage search (details)
Model #1320
Type: atomic / Software: (r8972/NA) / Radius of dummy atoms: 1.90 A / Chi-square value: 0.760
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: parDE-like toxin-antitoxin module, EcPaaA2_13-63-HisEcParE2 construct
Specimen concentration: 12 mg/ml / Entity id: 702 / 704
BufferName: 50 mM Tris-HCl, 500 mM NaCl / pH: 7.5
Entity #702Name: ParE2 / Type: protein / Description: Plasmid stabilization protein ParE / Formula weight: 12.596 / Num. of mol.: 1 / Source: Escherichia coli / References: UniProt: A0A0D7C2L1
Sequence:
MGSSHHHHHH SSGLVPRGSH LPVLWLESAD TDLDDITSYI ARFDIDAAER LWQRLRGCVL PLSEHPYLYP PSDRVPGLRE IVAHPNYIIL YRVTTSSVEV VNVIHARRQF
Entity #704Name: PaaA2 / Type: protein / Description: Uncharacterized protein / Formula weight: 6.231 / Num. of mol.: 1 / Source: Escherichia coli O157:H7 str. SS52 / References: UniProt: A0A0F6F6Q9
Sequence:
METIEQENSY NEWLRAKVAT SLADPRPAIP HDEVERRMAE RFAKMRKERS KQ

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Experimental information

BeamInstrument name: SOLEIL SWING / City: Saint-Aubin / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.103 Å / Dist. spec. to detc.: 1.82 mm
DetectorName: AVIEX / Type: CCD
Scan
Title: parDE-like toxin-antitoxin module, EcPaaA2_13-63-HisEcParE2 construct
Measurement date: Feb 5, 2012 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 0.75 sec. / Number of frames: 250 / Unit: 1/A /
MinMax
Q0.0238 0.4003
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 667 /
MinMax
Q0.0237825 0.400256
P(R) point1 667
R0 91.5
Result
Type of curve: other /
ExperimentalPorod
MW21.3 kDa21 kDa
Volume-35.7 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I00.02 0.01 0.0213863 0.01
Radius of gyration, Rg2.243 nm0.006 2.158 nm0.004

MinMaxError
D-9.3 0.5
Guinier point1 52 -

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