4ATO

New insights into the mechanism of bacterial Type III toxin-antitoxin systems: selective toxin inhibition by a non-coding RNA pseudoknot


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Selectivity and Self-Assembly in the Control of a Bacterial Toxin by an Antitoxic Noncoding RNA Pseudoknot.

Short, F.L.Pei, X.Y.Blower, T.R.Ong, S.L.Fineran, P.C.Luisi, B.F.Salmond, G.P.C.

(2013) Proc Natl Acad Sci U S A 110: E241

  • DOI: 10.1073/pnas.1216039110
  • Primary Citation of Related Structures:  
    4ATO

  • PubMed Abstract: 
  • Bacterial small RNAs perform numerous regulatory roles, including acting as antitoxic components in toxin-antitoxin systems. In type III toxin-antitoxin systems, small processed RNAs directly antagonize their toxin protein partners, and in the systems characterized the toxin and antitoxin components together form a trimeric assembly ...

    Bacterial small RNAs perform numerous regulatory roles, including acting as antitoxic components in toxin-antitoxin systems. In type III toxin-antitoxin systems, small processed RNAs directly antagonize their toxin protein partners, and in the systems characterized the toxin and antitoxin components together form a trimeric assembly. In the present study, we sought to define how the RNA antitoxin, ToxI, inhibits its potentially lethal protein partner, ToxN. We show through cross-inhibition experiments with the ToxIN systems from Pectobacterium atrosepticum (ToxIN(Pa)) and Bacillus thuringiensis (ToxIN(Bt)) that ToxI RNAs are highly selective enzyme inhibitors. Both systems have an "addictive" plasmid maintenance phenotype. We demonstrate that ToxI(Pa) can inhibit ToxN(Pa) in vitro both in its processed form and as a repetitive precursor RNA, and this inhibition is linked to the self-assembly of the trimeric complex. Inhibition and self-assembly are both mediated entirely by the ToxI(Pa) RNA, with no requirement for cellular factors or exogenous energy. Finally, we explain the origins of ToxI antitoxin selectivity through our crystal structure of the ToxIN(Bt) complex. Our results show how a processed RNA pseudoknot can inhibit a deleterious protein with exquisite molecular specificity and how these self-contained and addictive RNA-protein pairs can confer different adaptive benefits in their bacterial hosts.


    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TOXNA194Bacillus thuringiensisMutation(s): 0 
EC: 3.1
UniProt
Find proteins for Q3YN09 (Bacillus thuringiensis subsp. kurstaki)
Explore Q3YN09 
Go to UniProtKB:  Q3YN09
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3YN09
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
TOXIB [auth G]34Bacillus thuringiensis
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
C [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.1α = 90
b = 127.1β = 90
c = 37.735γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-01-09
    Changes: Database references
  • Version 1.2: 2013-01-30
    Changes: Database references
  • Version 1.3: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other