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- SASDC56: YtvA (dark/inactive state) (YtvA (pfyP - Blue light photoreceptor... -

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Basic information

Entry
Database: SASBDB / ID: SASDC56
SampleYtvA (dark/inactive state)
  • YtvA (pfyP - Blue light photoreceptor - Bacillus subtilis (strain 168) (protein), YtvA, Escherichia coli
Function / homology
Function and homology information


photoreceptor activity
Similarity search - Function
: / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) ...: / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
Blue-light photoreceptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
CitationJournal: J Mol Biol / Year: 2010
Title: The switch that does not flip: the blue-light receptor YtvA from Bacillus subtilis adopts an elongated dimer conformation independent of the activation state as revealed by a combined AUC and SAXS study.
Authors: Marcel Jurk / Matthias Dorn / Alexey Kikhney / Dmitri Svergun / Wolfgang Gärtner / Peter Schmieder /
Abstract: Photoreceptors play an important role in plants and bacteria by converting extracellular stimuli into intracellular signals. One distinct class are the blue-light-sensitive phototropins harboring a ...Photoreceptors play an important role in plants and bacteria by converting extracellular stimuli into intracellular signals. One distinct class are the blue-light-sensitive phototropins harboring a light-oxygen-voltage (LOV) domain coupled to various effector domains. Photon absorption by the chromophore within the LOV domain results in an activation of the output domain via mechanisms that are hitherto not well understood. The photoreceptor YtvA from Bacillus subtilis is a bacterial analog of phototropins, consists of an LOV and a sulfate transporter/anti-sigma factor antagonist domain, and is involved in the response of the bacterium to environmental stress. We present here analytical ultracentrifugation studies and small-angle X-ray scattering experiments, showing that YtvA is a dimer. On the basis of these results, we present a low-resolution model of the dimer in the dark and the lit state of the protein. In addition, we show that YtvA does not change its oligomerization state or its overall shape upon light activation.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Models

Model #1441
Type: dummy / Radius of dummy atoms: 1.90 A / Symmetry: P2 / Chi-square value: 16.74
Search similar-shape structures of this assembly by Omokage search (details)
Model #1400
Type: dummy / Radius of dummy atoms: 2.20 A / Symmetry: P2 / Chi-square value: 17.625
Search similar-shape structures of this assembly by Omokage search (details)
Model #1442
Type: dummy / Radius of dummy atoms: 2.75 A / Chi-square value: 17.625
Search similar-shape structures of this assembly by Omokage search (details)
Model #1401
Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 47.748
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: YtvA (dark/inactive state) / Specimen concentration: 1.70-11.00
BufferName: PBS + 5 mM DTT / pH: 7.4
Comment: 10 mM phosphate buffer; 2.7 mM KCl; 137 mM NaCl; 5 mM DTT
Entity #731Name: YtvA / Type: protein
Description: YtvA (pfyP - Blue light photoreceptor - Bacillus subtilis (strain 168)
Formula weight: 29.12 / Num. of mol.: 2 / Source: Escherichia coli / References: UniProt: O34627
Sequence: GASFQSFGIP GQLEVIKKAL DHVRVGVVIT DPALEDNPIV YVNQGFVQMT GYETEEILGK NCRFLQGKHT DPAEVDNIRT ALQNKEPVTV QIQNYKKDGT MFWNELNIDP MEIEDKTYFV GIQNDITKQK EYEKLLEDSL TEITALSTPI VPIRNGISAL PLVGNLTEER ...Sequence:
GASFQSFGIP GQLEVIKKAL DHVRVGVVIT DPALEDNPIV YVNQGFVQMT GYETEEILGK NCRFLQGKHT DPAEVDNIRT ALQNKEPVTV QIQNYKKDGT MFWNELNIDP MEIEDKTYFV GIQNDITKQK EYEKLLEDSL TEITALSTPI VPIRNGISAL PLVGNLTEER FNSIVCTLTN ILSTSKDDYL IIDLSGLAQV NEQTADQIFK LSHLLKLTGT ELIITGIKPE LAMKMNKLDA NFSSLKTYSN VKDAVKVLPI M

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Experimental information

BeamInstrument name: DORIS III X33 / City: Hamburg / 国: Germany / Shape: 0.6 / Type of source: X-ray synchrotron / Wavelength: 0.15 Å / Dist. spec. to detc.: 2.7 mm
DetectorName: Pilatus 1M-W / Pixsize x: 0.172 mm
Scan
Title: YtvA (dark/inactive state) / Measurement date: Oct 24, 2009 / Storage temperature: 4 °C / Cell temperature: 20 °C / Exposure time: 30 sec. / Number of frames: 4 / Unit: 1/nm /
MinMax
Q0.0775 6.237
Distance distribution function P(R)
Sofotware P(R): GNOM 4.5a / Number of points: 289 /
MinMax
Q0.2335 1.769
P(R) point59 347
R0 10.1
Result
Type of curve: extrapolated /
ExperimentalPorod
MW47 kDa47 kDa
Volume-75 nm3

P(R)GuinierGuinier error
Forward scattering, I069.98 71.16 -
Radius of gyration, Rg3.2 nm3.2 nm0.1

MinMaxError
D-10.1 1
Guinier point14 113 -

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