6G26

The crystal structure of the Burkholderia pseudomallei HicAB complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


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


Literature

The molecular basis of protein toxin HicA-dependent binding of the protein antitoxin HicB to DNA.

Winter, A.J., Williams, C., Isupov, M.N., Crocker, H., Gromova, M., Marsh, P., Wilkinson, O.J., Dillingham, M.S., Harmer, N.J., Titball, R.W., Crump, M.P.

(2018) J Biol Chem 293: 19429-19440

  • DOI: https://doi.org/10.1074/jbc.RA118.005173
  • Primary Citation of Related Structures:  
    6G1C, 6G1N, 6G26

  • PubMed Abstract: 

    • Toxin-antitoxin (TA) systems are present in many bacteria and play important roles in bacterial growth, physiology, and pathogenicity. Those that are best studied are the type II TA systems, in which both toxins and antitoxins are proteins. The HicAB system is one of the prototypic TA systems, found in many bacterial species ...

    Toxin-antitoxin (TA) systems are present in many bacteria and play important roles in bacterial growth, physiology, and pathogenicity. Those that are best studied are the type II TA systems, in which both toxins and antitoxins are proteins. The HicAB system is one of the prototypic TA systems, found in many bacterial species. Complex interactions between the protein toxin (HicA), the protein antitoxin (HicB), and the DNA upstream of the encoding genes regulate the activity of this system, but few structural details are available about how HicA destabilizes the HicB-DNA complex. Here, we determined the X-ray structures of HicB and the HicAB complex to 1.8 and 2.5 Å resolution, respectively, and characterized their DNA interactions. This revealed that HicB forms a tetramer and HicA and HicB form a heterooctameric complex that involves structural reorganization of the C-terminal (DNA-binding) region of HicB. Our observations indicated that HicA has a profound impact on binding of HicB to DNA sequences upstream of hicAB in a stoichiometric-dependent way. At low ratios of HicA:HicB, there was no effect on DNA binding, but at higher ratios, the affinity for DNA declined cooperatively, driving dissociation of the HicA:HicB:DNA complex. These results reveal the structural mechanisms by which HicA de-represses the HicB-DNA complex.

    Organizational Affiliation: 

    From the School of Chemistry, University of Bristol Cantock's Close, Bristol BS8 1TS, United Kingdom, Matt.crump@bristol.ac.uk.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HicB
A, B, C, D
142Burkholderia pseudomallei K96243Mutation(s): 0 
Gene Names: BPSS0391
UniProt
Find proteins for Q63NA5 (Burkholderia pseudomallei (strain K96243))
Explore Q63NA5 
Go to UniProtKB:  Q63NA5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63NA5
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HicA
E, F, G, H
64Burkholderia pseudomallei K96243Mutation(s): 0 
Gene Names: BPSS0390
UniProt
Find proteins for Q63NA6 (Burkholderia pseudomallei (strain K96243))
Explore Q63NA6 
Go to UniProtKB:  Q63NA6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63NA6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE
Download Ideal Coordinates CCD File 
EA [auth D]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
R [auth B],
W [auth C],
Z [auth D]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
FA [auth H]
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
FA [auth H],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
X [auth C],
Y [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.14α = 90
b = 74.19β = 90.05
c = 85.31γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
xia2data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J014400/1

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2019-11-06
    Changes: Data collection, Database references