4ML2

Crystal structure of wild-type YafQ


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Functional Characterization of Escherichia coli Toxin-Antitoxin Complex DinJ-YafQ

Liang, Y.Gao, Z.Wang, F.Zhang, Y.Dong, Y.Liu, Q.

(2014) J.Biol.Chem. 289: 21191-21202

  • DOI: 10.1074/jbc.M114.559773
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Toxin YafQ functions as a ribonuclease in the dinJ-yafQ toxin-antitoxin system of Escherichia coli. Antitoxin DinJ neutralizes YafQ-mediated toxicity by forming a stable protein complex. Here, crystal structures of the (DinJ)2-(YafQ)2 complex and the ...

    Toxin YafQ functions as a ribonuclease in the dinJ-yafQ toxin-antitoxin system of Escherichia coli. Antitoxin DinJ neutralizes YafQ-mediated toxicity by forming a stable protein complex. Here, crystal structures of the (DinJ)2-(YafQ)2 complex and the isolated YafQ toxin have been determined. The structure of the heterotetrameric complex (DinJ)2-(YafQ)2 revealed that the N-terminal region of DinJ folds into a ribbon-helix-helix motif and dimerizes for DNA recognition, and the C-terminal portion of each DinJ exclusively wraps around a YafQ molecule. Upon incorporation into the heterotetrameric complex, a conformational change of YafQ in close proximity to the catalytic site of the typical microbial ribonuclease fold was observed and validated. Mutagenesis experiments revealed that a DinJ mutant restored YafQ RNase activity in a tetramer complex in vitro but not in vivo. An electrophoretic mobility shift assay showed that one of the palindromic sequences present in the upstream intergenic region of DinJ served as a binding sequences for both the DinJ-YafQ complex and the antitoxin DinJ alone. Based on structure-guided and site-directed mutagenesis of DinJ-YafQ, we showed that two pairs of amino acids in DinJ were important for DNA binding; the R8A and K16A substitutions and the S31A and R35A substitutions in DinJ abolished the DNA binding ability of the DinJ-YafQ complex.


    Organizational Affiliation

    the Multidiscipline Research Center, Institute of High Energy Physics of the Chinese Academy of Sciences, 19B Yuequan Road, Beijing 100049, China, and dongyh@ihep.ac.cn.,the Key Laboratory of Molecular Biology on Infectious Disease, Chongqing Medical University, YiXueYuanlu-1, Chongqing 400016, China.,the Multidiscipline Research Center, Institute of High Energy Physics of the Chinese Academy of Sciences, 19B Yuequan Road, Beijing 100049, China, and liuqsh@ihep.ac.cn.,From the School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China, the Multidiscipline Research Center, Institute of High Energy Physics of the Chinese Academy of Sciences, 19B Yuequan Road, Beijing 100049, China, and.,the Multidiscipline Research Center, Institute of High Energy Physics of the Chinese Academy of Sciences, 19B Yuequan Road, Beijing 100049, China, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mRNA interferase YafQ
A
95Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: yafQ
EC: 3.1.-.-
Find proteins for Q47149 (Escherichia coli (strain K12))
Go to UniProtKB:  Q47149
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.176 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 41.299α = 90.00
b = 89.832β = 90.00
c = 75.015γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXrefinement
MAR345data collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2014-08-20
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description