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1,068,577 Computed Structure Models (CSM)
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 5FVJ|pdb_00005fvj

Crystal structure of TacT (tRNA acetylating toxin) from Salmonella


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.225 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

wwPDB Validation  3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

A Salmonella Toxin Promotes Persister Formation Through Acetylation of tRNA.

Cheverton, A.M.Gollan, B.Przydacz, M.Wong, C.T.Mylona, A.Hare, S.A.Helaine, S.

(2016) Mol Cell 63: 86

  • PubMed27264868 Search on PubMedSearch on PubMed Central
  • DOI: https://doi.org/10.1016/j.molcel.2016.05.002
  • Primary Citation of Related Structures:  
    5FVJ

  • PubMed Abstract: 

    The recalcitrance of many bacterial infections to antibiotic treatment is thought to be due to the presence of persisters that are non-growing, antibiotic-insensitive cells. Eventually, persisters resume growth, accounting for relapses of infection. Salmonella is an important pathogen that causes disease through its ability to survive inside macrophages. After macrophage phagocytosis, a significant proportion of the Salmonella population forms non-growing persisters through the action of toxin-antitoxin modules. Here we reveal that one such toxin, TacT, is an acetyltransferase that blocks the primary amine group of amino acids on charged tRNA molecules, thereby inhibiting translation and promoting persister formation. Furthermore, we report the crystal structure of TacT and note unique structural features, including two positively charged surface patches that are essential for toxicity. Finally, we identify a detoxifying mechanism in Salmonella wherein peptidyl-tRNA hydrolase counteracts TacT-dependent growth arrest, explaining how bacterial persisters can resume growth.


  • Organizational Affiliation

    Section of Microbiology, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK.

Biological Assembly 1  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (ACO)


Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 


Find Similar Assemblies

Biological assembly 1 assigned by authors and generated by PISA (software)

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Macromolecule Content

  • Total Structure Weight: 37.85 kDa 
  • Atom Count: 3,085 
  • Modelled Residue Count: 323 
  • Deposited Residue Count: 332 
  • Unique protein chains: 1

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PUTATIVE ACETYLTRANSFERASE166Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 1 
EC: 2.3.1
UniProt
Find proteins for A0A0F6B8D8 (Salmonella typhimurium (strain 14028s / SGSC 2262))
Explore A0A0F6B8D8 
Go to UniProtKB:  A0A0F6B8D8
Entity Groups 
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0F6B8D8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.225 (Depositor), 0.240 (DCC) 
  • R-Value Work: 0.172 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.4α = 90
b = 85.66β = 93.21
c = 55.32γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2016-06-22
    Changes: Database references
  • Version 1.2: 2016-07-20
    Changes: Database references
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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