7PCR

Helicobacter pylori RNase J


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Acetylation regulates the oligomerization state and activity of RNase J, the Helicobacter pylori major ribonuclease.

Tejada-Arranz, A.Lulla, A.Bouilloux-Lafont, M.Turlin, E.Pei, X.Y.Douche, T.Matondo, M.Williams, A.H.Raynal, B.Luisi, B.F.De Reuse, H.

(2023) Nat Commun 14: 8072-8072

  • DOI: https://doi.org/10.1038/s41467-023-43825-8
  • Primary Citation of Related Structures:  
    7PCR, 8CGL

  • PubMed 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 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.


  • Organizational Affiliation

    Département de Microbiologie, Unité Pathogenèse de Helicobacter, UMR CNRS 6047, Institut Pasteur, Paris, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease J553Helicobacter pylori 26695Mutation(s): 0 
Gene Names: rnjHP_1430
EC: 3.1
UniProt
Find proteins for P56185 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P56185 
Go to UniProtKB:  P56185
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56185
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.49α = 90
b = 158.49β = 90
c = 214.26γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom200873/Z/16/Z

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-25
    Type: Initial release
  • Version 1.1: 2023-12-27
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Refinement description