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- SASDCY4: RNase E 603-850 -

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Basic information

Entry
Database: SASBDB / ID: SASDCY4
SampleRNase E 603-850
  • RNase E 603-850 (protein), RNase E 603-850, Escherichia coli
Function / homologyRNase E
Function and homology information
Biological speciesEscherichia coli (E. coli)
CitationJournal: Nucleic Acids Res / Year: 2018
Title: Analysis of the natively unstructured RNA/protein-recognition core in the Escherichia coli RNA degradosome and its interactions with regulatory RNA/Hfq complexes.
Authors: Heather A Bruce / Dijun Du / Dijana Matak-Vinkovic / Katarzyna J Bandyra / R William Broadhurst / Esther Martin / Frank Sobott / Alexander V Shkumatov / Ben F Luisi /
Abstract: The RNA degradosome is a multi-enzyme assembly that plays a central role in the RNA metabolism of Escherichia coli and numerous other bacterial species including pathogens. At the core of the ...The RNA degradosome is a multi-enzyme assembly that plays a central role in the RNA metabolism of Escherichia coli and numerous other bacterial species including pathogens. At the core of the assembly is the endoribonuclease RNase E, one of the largest E. coli proteins and also one that bears the greatest region predicted to be natively unstructured. This extensive unstructured region, situated in the C-terminal half of RNase E, is punctuated with conserved short linear motifs that recruit partner proteins, direct RNA interactions, and enable association with the cytoplasmic membrane. We have structurally characterized a subassembly of the degradosome-comprising a 248-residue segment of the natively unstructured part of RNase E, the DEAD-box helicase RhlB and the glycolytic enzyme enolase, and provide evidence that it serves as a flexible recognition centre that can co-recruit small regulatory RNA and the RNA chaperone Hfq. Our results support a model in which the degradosome captures substrates and regulatory RNAs through the recognition centre, facilitates pairing to cognate transcripts and presents the target to the ribonuclease active sites of the greater assembly for cooperative degradation or processing.
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 #1299
Type: atomic / Software: (r8972/NA) / Radius of dummy atoms: 1.90 A / Chi-square value: 5.258 / P-value: 0.000002
Search similar-shape structures of this assembly by Omokage search (details)
Model #1300
Type: atomic / Software: (r8972/NA) / Radius of dummy atoms: 1.90 A / Chi-square value: 5.258 / P-value: 0.000002
Search similar-shape structures of this assembly by Omokage search (details)
Model #1301
Type: atomic / Software: (r8972/NA) / Radius of dummy atoms: 1.90 A / Chi-square value: 5.258 / P-value: 0.000002
Search similar-shape structures of this assembly by Omokage search (details)
Model #1302
Type: atomic / Software: (r8972/NA) / Radius of dummy atoms: 1.90 A / Chi-square value: 5.258 / P-value: 0.000002
Search similar-shape structures of this assembly by Omokage search (details)
Model #1303
Type: atomic / Software: (r8972/NA) / Radius of dummy atoms: 1.90 A / Chi-square value: 5.258 / P-value: 0.000002
Search similar-shape structures of this assembly by Omokage search (details)
Model #1304
Type: atomic / Software: (r8972/NA) / Radius of dummy atoms: 1.90 A / Chi-square value: 5.258 / P-value: 0.000002
Search similar-shape structures of this assembly by Omokage search (details)
Model #1305
Type: atomic / Software: (r8972/NA) / Radius of dummy atoms: 1.90 A / Chi-square value: 5.258 / P-value: 0.000002
Search similar-shape structures of this assembly by Omokage search (details)
Model #1306
Type: atomic / Software: (r8972/NA) / Radius of dummy atoms: 1.90 A / Chi-square value: 5.258 / P-value: 0.000002
Search similar-shape structures of this assembly by Omokage search (details)
Model #1307
Type: atomic / Software: (r8972/NA) / Radius of dummy atoms: 1.90 A / Chi-square value: 5.258 / P-value: 0.000002
Search similar-shape structures of this assembly by Omokage search (details)
Model #1308
Type: atomic / Software: (r8972/NA) / Radius of dummy atoms: 1.90 A / Chi-square value: 5.258 / P-value: 0.000002
Search similar-shape structures of this assembly by Omokage search (details)
Model #1309
Type: atomic / Software: (r8972/NA) / Radius of dummy atoms: 1.90 A / Chi-square value: 5.258 / P-value: 0.000002
Search similar-shape structures of this assembly by Omokage search (details)
Model #1310
Type: atomic / Software: (r8972/NA) / Radius of dummy atoms: 1.90 A / Chi-square value: 5.258 / P-value: 0.000002
Search similar-shape structures of this assembly by Omokage search (details)
Model #1311
Type: atomic / Software: (r8972/NA) / Radius of dummy atoms: 1.90 A / Chi-square value: 5.258 / P-value: 0.000002
Search similar-shape structures of this assembly by Omokage search (details)
Model #1312
Type: atomic / Software: (r8972/NA) / Radius of dummy atoms: 1.90 A / Chi-square value: 5.258 / P-value: 0.000002
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: RNase E 603-850 / Specimen concentration: 12 mg/ml
BufferName: 50 mM Tris HCl, 100 mM NaCl, 100 mM KCl, 10 mM MgCl2, 10 mM DTT and 5 % glycerol (v/v)
pH: 7.5
Entity #697Name: RNase E 603-850 / Type: protein / Description: RNase E 603-850 / Formula weight: 30.127 / Num. of mol.: 1 / Source: Escherichia coli / References: UniProt: Q46977
Sequence: ERQQDRRKPR QNNRRDRNER RDTRSERTEG SDNREENRRN RRQAQQQTAE TRESRQQAEV TEKARTADEQ QAPRRERSRR RNDDKRQAQQ EAKALNVEEQ SVQETEQEER VRPVQPRRKQ RQLNQKVRYE QSVAEEAVVA PVVEETVAAE PIVQEAPAPR TELVKVPLPV ...Sequence:
ERQQDRRKPR QNNRRDRNER RDTRSERTEG SDNREENRRN RRQAQQQTAE TRESRQQAEV TEKARTADEQ QAPRRERSRR RNDDKRQAQQ EAKALNVEEQ SVQETEQEER VRPVQPRRKQ RQLNQKVRYE QSVAEEAVVA PVVEETVAAE PIVQEAPAPR TELVKVPLPV VAQTAPEQQE ENNADNRDNG GMPRRSRRSP RHLRVSGQRR RRYRDERYPT QSPMPLTVAC ASPELASGKV WIRYPIVRHH HHHH

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Experimental information

BeamInstrument name: SOLEIL SWING / City: Saint-Aubin / 国: France / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.1022 Å / Dist. spec. to detc.: 1.79 mm
DetectorName: AVIEX PCCD170170 / Type: CCD
Scan
Title: RNase E 603-850 / Measurement date: Dec 5, 2014 / Storage temperature: 15 °C / Cell temperature: 15 °C / Exposure time: 1.5 sec. / Number of frames: 250 / Unit: 1/A /
MinMax
Q0.0063 0.5703
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 427 /
MinMax
Q0.00797823 0.250585
P(R) point1 427
R0 275
Result
Type of curve: other /
ExperimentalPorod
MW49 kDa81.8 kDa
Volume-139 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I00.05 0.01 0.049 0.01
Radius of gyration, Rg5.742 nm0.014 5.255 nm0.031

MinMaxError
D-27.5 1
Guinier point10 28 -

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