6Y2P

Escherichia coli RnlA-RnlB Toxin-Antitoxin System.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Alternative dimerization is required for activity and inhibition of the HEPN ribonuclease RnlA.

Garcia-Rodriguez, G.Charlier, D.Wilmaerts, D.Michiels, J.Loris, R.

(2021) Nucleic Acids Res 49: 7164-7178

  • DOI: https://doi.org/10.1093/nar/gkab513
  • Primary Citation of Related Structures:  
    6Y2P, 6Y2Q, 6Y2R, 7AEX

  • PubMed Abstract: 

    The rnlAB toxin-antitoxin operon from Escherichia coli functions as an anti-phage defense system. RnlA was identified as a member of the HEPN (Higher Eukaryotes and Prokaryotes Nucleotide-binding domain) superfamily of ribonucleases. The activity of the toxin RnlA requires tight regulation by the antitoxin RnlB, the mechanism of which remains unknown. Here we show that RnlA exists in an equilibrium between two different homodimer states: an inactive resting state and an active canonical HEPN dimer. Mutants interfering with the transition between states show that canonical HEPN dimerization via the highly conserved RX4-6H motif is required for activity. The antitoxin RnlB binds the canonical HEPN dimer conformation, inhibiting RnlA by blocking access to its active site. Single-alanine substitutions mutants of the highly conserved R255, E258, R318 and H323 show that these residues are involved in catalysis and substrate binding and locate the catalytic site near the dimer interface of the canonical HEPN dimer rather than in a groove located between the HEPN domain and the preceding TBP-like domain. Overall, these findings elucidate the structural basis of the activity and inhibition of RnlA and highlight the crucial role of conformational heterogeneity in protein function.


  • Organizational Affiliation

    Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050 Brussel, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA endoribonuclease toxin LS
A, B
357Escherichia coli K-12Mutation(s): 0 
Gene Names: rnlAstdyfjNb2630JW2611
EC: 3.1
UniProt
Find proteins for P52129 (Escherichia coli (strain K12))
Explore P52129 
Go to UniProtKB:  P52129
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52129
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Antitoxin RnlB
C, D
134Escherichia coli K-12Mutation(s): 0 
Gene Names: rnlByfjOb2631JW5418
UniProt
Find proteins for P52130 (Escherichia coli (strain K12))
Explore P52130 
Go to UniProtKB:  P52130
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52130
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 243.32α = 90
b = 133.58β = 95.11
c = 55.64γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
MR-Rosettaphasing
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)BelgiumG.0B25.15N

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2021-07-21
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description