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- PDB-7pcr: Helicobacter pylori RNase J -

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Basic information

Entry
Database: PDB / ID: 7pcr
TitleHelicobacter pylori RNase J
ComponentsRibonuclease J
KeywordsHYDROLASE / RNase J / Helicobacter pylori / RNA metabolism
Function / homology
Function and homology information


5'-3' RNA exonuclease activity / RNA endonuclease activity / rRNA processing / protein homotetramerization / Hydrolases; Acting on ester bonds / protein homodimerization activity / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Ribonuclease J, conserved site / Uncharacterized protein family UPF0036 signature. / Ubiquitin-like (UB roll) - #580 / Metallo-hydrolase/oxidoreductase / Ribonuclease J, bacteria / Ribonuclease J, C-terminal / Ribonuclease J C-terminal domain / Ribonuclease J, beta-CASP domain / Ribonuclease J / Ribonuclease J, domain 2 ...Ribonuclease J, conserved site / Uncharacterized protein family UPF0036 signature. / Ubiquitin-like (UB roll) - #580 / Metallo-hydrolase/oxidoreductase / Ribonuclease J, bacteria / Ribonuclease J, C-terminal / Ribonuclease J C-terminal domain / Ribonuclease J, beta-CASP domain / Ribonuclease J / Ribonuclease J, domain 2 / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Ubiquitin-like (UB roll) / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLuisi, B.F. / Pei, X.Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust200873/Z/16/Z United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Acetylation regulates the oligomerization state and activity of RNase J, the Helicobacter pylori major ribonuclease.
Authors: Alejandro Tejada-Arranz / Aleksei Lulla / Maxime Bouilloux-Lafont / Evelyne Turlin / Xue-Yuan Pei / Thibaut Douché / Mariette Matondo / Allison H Williams / Bertrand Raynal / Ben F Luisi / Hilde De Reuse /
Abstract: In the gastric pathogen Helicobacter pylori, post-transcriptional regulation relies strongly on the activity of the essential ribonuclease RNase J. Here, we elucidated the crystal and cryo-EM ...In the gastric pathogen Helicobacter pylori, post-transcriptional regulation relies strongly on the activity of the essential ribonuclease RNase J. Here, we elucidated the crystal and cryo-EM structures of RNase J and determined that it assembles into dimers and tetramers in vitro. We found that RNase J extracted from H. pylori is acetylated on multiple lysine residues. Alanine substitution of several of these residues impacts on H. pylori morphology, and thus on RNase J function in vivo. Mutations of Lysine 649 modulates RNase J oligomerization in vitro, which in turn influences ribonuclease activity in vitro. Our structural analyses of RNase J reveal loops that gate access to the active site and rationalizes how acetylation state of K649 can influence activity. We propose acetylation as a regulatory level controlling the activity of RNase J and its potential cooperation with other enzymes of RNA metabolism in H. pylori.
History
DepositionAug 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease J


Theoretical massNumber of molelcules
Total (without water)61,5031
Polymers61,5031
Non-polymers00
Water18010
1
A: Ribonuclease J

A: Ribonuclease J


Theoretical massNumber of molelcules
Total (without water)123,0052
Polymers123,0052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_445-y-1/2,-x-1/2,-z+1/21
Buried area2790 Å2
ΔGint-19 kcal/mol
Surface area44600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.490, 158.490, 214.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Ribonuclease J / RNase J


Mass: 61502.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: ATCC 700392 / 26695 / Gene: rnj, HP_1430 / Production host: Escherichia coli (E. coli)
References: UniProt: P56185, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 4.33 Å3/Da / Density % sol: 71.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 25% polyethylene glycol 1000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.75→56.03 Å / Num. obs: 35677 / % possible obs: 99.89 % / Redundancy: 3.6 % / Biso Wilson estimate: 75.81 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.081 / Rsym value: 0.16 / Net I/σ(I): 5.9
Reflection shellResolution: 2.75→2.848 Å / Num. unique obs: 3497 / CC1/2: 0.453

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bk2

3bk2


Resolution: 2.75→56.03 Å / SU ML: 0.4279 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.4715
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2672 1805 5.1 %
Rwork0.2455 33614 -
obs0.2467 35419 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 111.78 Å2
Refinement stepCycle: LAST / Resolution: 2.75→56.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4058 0 0 10 4068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00834145
X-RAY DIFFRACTIONf_angle_d1.21235628
X-RAY DIFFRACTIONf_chiral_restr0.0683652
X-RAY DIFFRACTIONf_plane_restr0.0062730
X-RAY DIFFRACTIONf_dihedral_angle_d17.08351469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.820.40411220.36622552X-RAY DIFFRACTION98.82
2.82-2.910.36651170.34072555X-RAY DIFFRACTION99.63
2.91-30.35861300.32352590X-RAY DIFFRACTION99.52
3-3.110.29661560.31382546X-RAY DIFFRACTION99.48
3.11-3.230.35821430.30482541X-RAY DIFFRACTION99.22
3.23-3.380.33161190.27782557X-RAY DIFFRACTION98.71
3.38-3.560.30141280.25772576X-RAY DIFFRACTION99.67
3.56-3.780.27491430.23072592X-RAY DIFFRACTION99.24
3.78-4.070.24821500.22042559X-RAY DIFFRACTION99.01
4.07-4.480.22941550.19442573X-RAY DIFFRACTION99.27
4.48-5.130.21711380.19292605X-RAY DIFFRACTION99.1
5.13-6.460.23611550.25922622X-RAY DIFFRACTION99.21
6.46-56.030.26491490.24982746X-RAY DIFFRACTION98.57
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)
11.50611899921-0.0484153104716-0.3028897459240.990073982913-0.5384120702272.108708475730.00235896392240.0874901575203-0.122803161484-0.108917497157-0.106621288198-0.03277996692170.1994524371450.08626345974930.1034469364720.398451057265-0.0325088229808-0.1029054833620.525595796224-0.01419096578230.45928534133-50.9532402068-1.6818245923260.4734796364
21.963508568512.53442362399-1.259121768933.41006268307-1.21139005524.03295819914-2.271535615211.32659830597-1.125466530520.120060547070.936836187387-1.178603216911.817364635050.286170617481.082534884762.39195370324-0.04628401248380.2940858249791.30176817524-0.309008966692.37082275718-38.1515193885-50.295728082745.618500306
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 139 through 599)
2X-RAY DIFFRACTION2(chain 'A' and resid 600 through 691)

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