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- PDB-5ohg: enolase in complex with RNase E -

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Basic information

Entry
Database: PDB / ID: 5ohg
Titleenolase in complex with RNase E
Components
  • (Ribonuclease ...) x 2
  • Enolase
KeywordsLYASE / enolase / RNase E
Function / homology
Function and homology information


regulation of RNA helicase activity / rRNA 5'-end processing / ribonuclease E / ribonuclease E activity / bacterial degradosome / endoribonuclease complex / DEAD/H-box RNA helicase binding / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity ...regulation of RNA helicase activity / rRNA 5'-end processing / ribonuclease E / ribonuclease E activity / bacterial degradosome / endoribonuclease complex / DEAD/H-box RNA helicase binding / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / 7S RNA binding / RNA catabolic process / tRNA processing / mRNA catabolic process / RNA nuclease activity / RNA processing / RNA endonuclease activity / glycolytic process / cytoplasmic side of plasma membrane / rRNA processing / protein complex oligomerization / protein homotetramerization / tRNA binding / rRNA binding / molecular adaptor activity / cytoskeleton / magnesium ion binding / cell surface / protein homodimerization activity / RNA binding / zinc ion binding / extracellular region / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Polyribonucleotide phosphorylase C-terminal / Polyribonucleotide phosphorylase C terminal / : / RNase E/G, Thioredoxin-like domain / Ribonuclease E/G / RNA-binding protein AU-1/Ribonuclease E/G / Ribonuclease E / Ribonuclease E/G family / Enolase / Enolase, conserved site ...Polyribonucleotide phosphorylase C-terminal / Polyribonucleotide phosphorylase C terminal / : / RNase E/G, Thioredoxin-like domain / Ribonuclease E/G / RNA-binding protein AU-1/Ribonuclease E/G / Ribonuclease E / Ribonuclease E/G family / Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / S1 domain profile. / Enolase-like; domain 1 / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding, OB-fold / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Enolase / Ribonuclease E
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 Å
AuthorsDu, D. / Luisi, B.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
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.
History
DepositionJul 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Database references
Category: citation / citation_author / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enolase
B: Enolase
C: Ribonuclease E
H: Enolase
I: Enolase
J: Ribonuclease E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,64019
Polymers191,0486
Non-polymers59213
Water30,1931676
1
A: Enolase
B: Enolase
C: Ribonuclease E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9199
Polymers95,6343
Non-polymers2856
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-94 kcal/mol
Surface area28020 Å2
MethodPISA
2
H: Enolase
I: Enolase
J: Ribonuclease E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,72110
Polymers95,4133
Non-polymers3087
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint-105 kcal/mol
Surface area28020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.683, 116.923, 107.776
Angle α, β, γ (deg.)90.00, 105.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABHI

#1: Protein
Enolase / / 2-phospho-D-glycerate hydro-lyase / 2-phosphoglycerate dehydratase


Mass: 45709.812 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: eno, b2779, JW2750 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6P9, phosphopyruvate hydratase

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Ribonuclease ... , 2 types, 2 molecules CJ

#2: Protein/peptide Ribonuclease E / / RNase E


Mass: 4214.870 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RNase E
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: rne, ams, hmp1, b1084, JW1071 / Production host: Escherichia coli (E. coli) / References: UniProt: P21513, ribonuclease E
#3: Protein/peptide Ribonuclease E / / RNase E


Mass: 3993.634 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: rne, ams, hmp1, b1084, JW1071 / Production host: Escherichia coli (E. coli) / References: UniProt: P21513, ribonuclease E

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Non-polymers , 4 types, 1689 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1676 / 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: 2.37 Å3/Da / Density % sol: 48.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M potassium thiocyanate, 0.1 M Bis-Tris propane (pH 8.5) and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.997→40 Å / Num. all: 121616 / Num. obs: 118999 / % possible obs: 98.59 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.061 / Net I/σ(I): 9.2
Reflection shellResolution: 1.99→2.09 Å / Rmerge(I) obs: 0.301 / Rpim(I) all: 0.191

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2fym

2fym


Resolution: 1.997→39.244 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.07
RfactorNum. reflection% reflection
Rfree0.197 5975 5.02 %
Rwork0.1607 --
obs0.1625 118999 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.997→39.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13333 0 29 1676 15038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813734
X-RAY DIFFRACTIONf_angle_d1.09718504
X-RAY DIFFRACTIONf_dihedral_angle_d13.448336
X-RAY DIFFRACTIONf_chiral_restr0.0582097
X-RAY DIFFRACTIONf_plane_restr0.0062421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9972-2.01990.26691920.20863487X-RAY DIFFRACTION92
2.0199-2.04360.23071870.19823819X-RAY DIFFRACTION100
2.0436-2.06850.23082130.19323827X-RAY DIFFRACTION100
2.0685-2.09470.25811930.19043804X-RAY DIFFRACTION100
2.0947-2.12230.21832260.18393779X-RAY DIFFRACTION100
2.1223-2.15140.2342160.17853779X-RAY DIFFRACTION100
2.1514-2.18210.20862140.17143788X-RAY DIFFRACTION100
2.1821-2.21470.22561840.1813826X-RAY DIFFRACTION100
2.2147-2.24930.37491850.33553262X-RAY DIFFRACTION86
2.2493-2.28610.33291590.31373202X-RAY DIFFRACTION84
2.2861-2.32560.22232030.17593824X-RAY DIFFRACTION100
2.3256-2.36780.23611960.16743840X-RAY DIFFRACTION100
2.3678-2.41340.20272070.16493791X-RAY DIFFRACTION100
2.4134-2.46260.24591880.1633810X-RAY DIFFRACTION100
2.4626-2.51620.21472040.16873830X-RAY DIFFRACTION100
2.5162-2.57470.19622010.16273853X-RAY DIFFRACTION100
2.5747-2.63910.18842000.15973773X-RAY DIFFRACTION100
2.6391-2.71040.19491970.15633831X-RAY DIFFRACTION100
2.7104-2.79010.19492050.15373835X-RAY DIFFRACTION100
2.7901-2.88020.19342260.14953795X-RAY DIFFRACTION100
2.8802-2.98310.18812140.15253795X-RAY DIFFRACTION100
2.9831-3.10250.18412030.1573818X-RAY DIFFRACTION100
3.1025-3.24360.18332170.15553851X-RAY DIFFRACTION100
3.2436-3.41450.18761930.15473814X-RAY DIFFRACTION100
3.4145-3.62830.17651830.14693767X-RAY DIFFRACTION98
3.6283-3.90820.16761970.14373766X-RAY DIFFRACTION98
3.9082-4.30110.15712000.12943819X-RAY DIFFRACTION99
4.3011-4.92240.16221870.12583865X-RAY DIFFRACTION100
4.9224-6.19780.19191990.15293857X-RAY DIFFRACTION100
6.1978-39.25110.17141860.15253917X-RAY DIFFRACTION99

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