6HPB | pdb_00006hpb

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 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.241 (Depositor), 0.224 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6HPB

This is version 1.2 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: https://doi.org/10.1016/j.str.2019.08.008
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 44.97 kDa 
  • Atom Count: 3,212 
  • Modeled Residue Count: 385 
  • Deposited Residue Count: 392 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
mRNA interferase toxin HicA
A, C
58Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
Gene Names: hicAyncNb4532JW5230
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
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Antitoxin HicB
B, D
138Escherichia coli 2-222-05_S4_C3Mutation(s): 0 
Gene Names: hicBydcQb1438JW1433
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
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free:  0.273 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.241 (Depositor), 0.224 (DCC) 
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  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Advisory, Data collection, Database references, Structure summary