4Q2U

Crystal structure of the E. coli DinJ-YafQ toxin-antitoxin complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Mechanisms of Toxin Inhibition and Transcriptional Repression by Escherichia coli DinJ-YafQ.

Ruangprasert, A., Maehigashi, T., Miles, S.J., Giridharan, N., Liu, J.X., Dunham, C.M.

(2014) J.Biol.Chem. 289: 20559-20569

  • DOI: 10.1074/jbc.M114.573006

  • PubMed Abstract: 

    • Bacteria encounter environmental stresses that regulate a gene expression program required for adaptation and survival. Here, we report the 1.8-Å crystal structure of the Escherichia coli toxin-antitoxin complex YafQ-(DinJ)2-YafQ, a key component of ...

    Bacteria encounter environmental stresses that regulate a gene expression program required for adaptation and survival. Here, we report the 1.8-Å crystal structure of the Escherichia coli toxin-antitoxin complex YafQ-(DinJ)2-YafQ, a key component of the stress response. The antitoxin DinJ dimer adopts a ribbon-helix-helix motif required for transcriptional autorepression, and toxin YafQ contains a microbial RNase fold whose proposed active site is concealed by DinJ binding. Contrary to previous reports, our studies indicate that equivalent levels of transcriptional repression occur by direct interaction of either YafQ-(DinJ)2-YafQ or a DinJ dimer at a single inverted repeat of its recognition sequence that overlaps with the -10 promoter region. Surprisingly, multiple YafQ-(DinJ)2-YafQ complexes binding to the operator region do not appear to amplify the extent of repression. Our results suggest an alternative model for transcriptional autorepression that may be novel to DinJ-YafQ.

    Organizational Affiliation: 

    From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322.,From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 christine.m.dunham@emory.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antitoxin DinJ
A, C, E, G, I, K, M, O
86Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: dinJ
Find proteins for Q47150 (Escherichia coli (strain K12))
Go to UniProtKB:  Q47150
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
mRNA interferase YafQ
B, D, F, H, J, L, N, P
102Escherichia 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, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 176.540α = 90.00
b = 120.920β = 130.77
c = 120.830γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PHENIXphasing
SHELXDphasing
PHENIXmodel building
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2014-07-02
    Type: Database references
  • Version 1.2: 2014-08-06
    Type: Database references