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:  
    6HPC, 6HPB

  • 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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
mRNA interferase toxin HicAAC58Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
Gene Names: hicAyncNb4532JW5230
EC: 3.1
Find proteins for P76106 (Escherichia coli (strain K12))
Explore P76106 
Go to UniProtKB:  P76106
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Antitoxin HicBBD138Escherichia coli 2-222-05_S4_C3Mutation(s): 0 
Gene Names: hicBydcQb1438JW1433
Find proteins for P67697 (Escherichia coli (strain K12))
Explore P67697 
Go to UniProtKB:  P67697
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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,CL-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 = 100α = 90
b = 100β = 90
c = 88.9γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



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
    Changes: Database references