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 

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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:  
    6HPB, 6HPC

  • 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, while HicB antitoxins contain a partial RNase H fold and either a helix-turn-helix (HTH) or ribbon-helix-helix domain ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
mRNA interferase toxin HicAA, C58Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
Gene Names: hicA, yncN, b4532, JW5230
EC: 3.1
UniProt
Find proteins for P76106 (Escherichia coli (strain K12))
Explore P76106 
Go to UniProtKB:  P76106
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76106
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Antitoxin HicBB, D138Escherichia coli 2-222-05_S4_C3Mutation(s): 0 
Gene Names: hicB, ydcQ, b1438, JW1433
UniProt
Find proteins for P67697 (Escherichia coli (strain K12))
Explore P67697 
Go to UniProtKB:  P67697
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP67697
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth D]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A, C 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 = 100α = 90
b = 100β = 90
c = 88.9γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF17OC0030646
Danish National Research FoundationDenmarkDNRF120

Revision History  (Full details and data files)

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