6AJM

Crystal structure of apo AtaTR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

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This is version 1.4 of the entry. See complete history


Literature

Crystal Structure of the Enterohemorrhagic Escherichia coli AtaT-AtaR Toxin-Antitoxin Complex.

Yashiro, Y.Yamashita, S.Tomita, K.

(2019) Structure 27: 476

  • DOI: https://doi.org/10.1016/j.str.2018.11.005
  • Primary Citation of Related Structures:  
    6AJM, 6AJN

  • PubMed Abstract: 

    AtaT-AtaR is an enterohemorrhagic Escherichia coli toxin-antitoxin system that modulates cellular growth under stress conditions. AtaT and AtaR act as a toxin and its repressor, respectively. AtaT is a member of the GNAT family, and the dimeric AtaT acetylates the α-amino group of the aminoacyl moiety of methionyl initiator tRNA fMet , thereby inhibiting translation initiation. The crystallographic analysis of the AtaT-AtaR complex revealed that the AtaT-AtaR proteins form a heterohexameric [AtaT-(AtaR 4 )-AtaT] complex, where two V-shaped AtaR dimers bridge two AtaT molecules. The N-terminal region of AtaR is required for its dimerization, and the C-terminal region of AtaR interacts with AtaT. The two AtaT molecules are spatially separated in the AtaT-AtaR complex. AtaT alone forms a dimer in solution, which is enzymatically active. The present structure, in which AtaR prevents AtaT from forming an active dimer, reveals the molecular basis of the AtaT toxicity repression by the antitoxin AtaR.


  • Organizational Affiliation

    Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acetyltransferase
A, B
183Escherichia coliMutation(s): 0 
Gene Names: BWP17_00640CVH05_12355
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DUF1778 domain-containing protein
C, D, E, F
88Escherichia coliMutation(s): 0 
Gene Names: 
UniProt
Find proteins for J7QA90 (Escherichia coli)
Explore J7QA90 
Go to UniProtKB:  J7QA90
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ7QA90
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
G [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.09α = 90
b = 116.42β = 90
c = 77.49γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan18H03980
Japan Science and TechnologyJapan26113002

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-02
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2019-02-13
    Changes: Data collection, Database references
  • Version 1.3: 2019-03-20
    Changes: Data collection, Database references
  • Version 1.4: 2023-11-22
    Changes: Data collection, Database references, Refinement description