6HPB

Crystal structure of the E.coli HicAB toxin-antitoxin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The E. coli HicB Antitoxin Contains a Structurally Stable Helix-Turn-Helix DNA Binding Domain.

Manav, M.C.Turnbull, K.J.Jurenas, D.Garcia-Pino, A.Gerdes, K.Brodersen, D.E.

(2019) Structure 27: 1675-1685.e3

  • DOI: 10.1016/j.str.2019.08.008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The E. coli hicAB type II toxin-antitoxin locus is unusual by being controlled by two promoters and by having the toxin encoded upstream of the antitoxin. HicA toxins contain a double-stranded RNA-binding fold and cleaves both mRNA and tmRNA in vivo, ...

    The E. coli hicAB type II toxin-antitoxin locus is unusual by being controlled by two promoters and by having the toxin encoded upstream of the antitoxin. HicA toxins contain a double-stranded RNA-binding fold and cleaves both mRNA and tmRNA in vivo, while HicB antitoxins contain a partial RNase H fold and either a helix-turn-helix (HTH) or ribbon-helix-helix domain. It is not known how an HTH DNA-binding domain affects higher-order structure for the HicAB modules. Here, we present crystal structures of the isolated E. coli HicB antitoxin and full-length HicAB complex showing that HicB forms a stable DNA-binding module and interacts in a canonical way with HicA despite the presence of an HTH-type DNA-binding domain. No major structural rearrangements take place upon binding of the toxin. Both structures expose well-ordered DNA-binding motifs allowing a model for DNA binding by the antitoxin to be generated.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Aarhus University, Centre for Bacterial Stress Response and Persistence, Aarhus 8000, Denmark. Electronic address: deb@mbg.au.dk.,Department of Biology, University of Copenhagen, Centre for Bacterial Stress Response and Persistence, Copenhagen 2200, Denmark.,Cellular and Molecular Microbiology, Université Libre de Bruxelles, Gosselies 6041, Belgium.,Department of Molecular Biology and Genetics, Aarhus University, Centre for Bacterial Stress Response and Persistence, Aarhus 8000, Denmark.,Cellular and Molecular Microbiology, Université Libre de Bruxelles, Gosselies 6041, Belgium; Walloon Excellence in Life Sciences and Biotechnology (WELBIO), Brussels, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mRNA interferase toxin HicA
A, C
58Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: hicA (yncN)
EC: 3.1.-.-
Find proteins for P76106 (Escherichia coli (strain K12))
Go to UniProtKB:  P76106
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antitoxin HicB
B, D
138Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: hicB (ydcQ)
Find proteins for P67697 (Escherichia coli (strain K12))
Go to UniProtKB:  P67697
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.241 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 100.000α = 90.00
b = 100.000β = 90.00
c = 88.900γ = 120.00
Software Package:
Software NamePurpose
AutoSolphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF17OC0030646
Danish National Research FoundationDenmarkDNRF120

Revision History 

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-11-13
    Type: Database references