6AJM

Crystal structure of apo AtaTR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.604 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1016/j.str.2018.11.005
  • Primary Citation of Related Structures:  

  • 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 ...

    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. Electronic address: kozo-tomita@cbms.k.u-tokyo.ac.jp.,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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-acetyltransferase
A, B
183Escherichia coliMutation(s): 0 
Find proteins for A0A1V3CQ74 (Escherichia coli)
Go to UniProtKB:  A0A1V3CQ74
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DUF1778 domain-containing protein
C, D, E, F
88Escherichia coliMutation(s): 0 
Gene Names: ybl13 (ybl13_1)
Find proteins for J7QA90 (Escherichia coli)
Go to UniProtKB:  J7QA90
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download SDF File 
Download CCD File 
B
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.604 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 101.090α = 90.00
b = 116.420β = 90.00
c = 77.490γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2019-01-02
    Type: Initial release
  • Version 1.1: 2019-01-23
    Type: Data collection, Database references, Structure summary
  • Version 1.2: 2019-02-13
    Type: Data collection, Database references
  • Version 1.3: 2019-03-20
    Type: Data collection, Database references