7CHD

AtaT complexed with acetyl-methionyl-tRNAfMet


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.286 
  • R-Value Observed: 0.289 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanism of aminoacyl-tRNA acetylation by an aminoacyl-tRNA acetyltransferase AtaT from enterohemorrhagic E. coli.

Yashiro, Y.Sakaguchi, Y.Suzuki, T.Tomita, K.

(2020) Nat Commun 11: 5438-5438

  • DOI: 10.1038/s41467-020-19281-z
  • Primary Citation of Related Structures:  
    7CHD

  • PubMed Abstract: 
  • Toxin-antitoxin systems in bacteria contribute to stress adaptation, dormancy, and persistence. AtaT, a type-II toxin in enterohemorrhagic E. coli, reportedly acetylates the α-amino group of the aminoacyl-moiety of initiator Met-tRNAf Met , thus inhibiting translation initiation ...

    Toxin-antitoxin systems in bacteria contribute to stress adaptation, dormancy, and persistence. AtaT, a type-II toxin in enterohemorrhagic E. coli, reportedly acetylates the α-amino group of the aminoacyl-moiety of initiator Met-tRNAf Met , thus inhibiting translation initiation. Here, we show that AtaT has a broader specificity for aminoacyl-tRNAs than initially claimed. AtaT efficiently acetylates Gly-tRNA Gly , Trp-tRNA Trp , Tyr-tRNA Tyr and Phe-tRNA Phe isoacceptors, in addition to Met-tRNAf Met , and inhibits global translation. AtaT interacts with the acceptor stem of tRNAf Met , and the consecutive G-C pairs in the bottom-half of the acceptor stem are required for acetylation. Consistently, tRNA Gly , tRNA Trp , tRNA Tyr and tRNA Phe also possess consecutive G-C base-pairs in the bottom halves of their acceptor stems. Furthermore, misaminoacylated valyl-tRNAf Met and isoleucyl-tRNAf Met are not acetylated by AtaT. Therefore, the substrate selection by AtaT is governed by the specific acceptor stem sequence and the properties of the aminoacyl-moiety of aminoacyl-tRNAs.


    Organizational Affiliation

    Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan. kozo-tomita@edu.k.u-tokyo.ac.jp.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-acetyltransferase domain-containing proteinABCDEFGH183Escherichia coli O157:H7Mutation(s): 1 
Gene Names: Z4832
Find proteins for Q8XED1 (Escherichia coli O157:H7)
Explore Q8XED1 
Go to UniProtKB:  Q8XED1
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (77-MER)I, J77Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.286 
  • R-Value Observed: 0.289 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 269.83α = 90
b = 68.28β = 90
c = 136.18γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanLS136
Japan Society for the Promotion of Science (JSPS)Japan18H03980
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan26113002
Japan Society for the Promotion of Science (JSPS)Japan19K16069

Revision History 

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references
  • Version 1.2: 2020-11-18
    Changes: Derived calculations