5IWH

Structure of P. vulgaris HigB toxin delta H92


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.101 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mechanism of endonuclease cleavage by the HigB toxin.

Schureck, M.A.Repack, A.Miles, S.J.Marquez, J.Dunham, C.M.

(2016) Nucleic Acids Res. 44: 7944-7953

  • DOI: 10.1093/nar/gkw598
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacteria encode multiple type II toxin-antitoxin modules that cleave ribosome-bound mRNAs in response to stress. All ribosome-dependent toxin family members structurally characterized to date adopt similar microbial RNase architectures despite posses ...

    Bacteria encode multiple type II toxin-antitoxin modules that cleave ribosome-bound mRNAs in response to stress. All ribosome-dependent toxin family members structurally characterized to date adopt similar microbial RNase architectures despite possessing low sequence identities. Therefore, determining which residues are catalytically important in this specialized RNase family has been a challenge in the field. Structural studies of RelE and YoeB toxins bound to the ribosome provided significant insights but biochemical experiments with RelE were required to clearly demonstrate which residues are critical for acid-base catalysis of mRNA cleavage. Here, we solved an X-ray crystal structure of the wild-type, ribosome-dependent toxin HigB bound to the ribosome revealing potential catalytic residues proximal to the mRNA substrate. Using cell-based and biochemical assays, we further determined that HigB residues His54, Asp90, Tyr91 and His92 are critical for activity in vivo, while HigB H54A and Y91A variants have the largest effect on mRNA cleavage in vitro Comparison of X-ray crystal structures of two catalytically inactive HigB variants with 70S-HigB bound structures reveal that HigB active site residues undergo conformational rearrangements likely required for recognition of its mRNA substrate. These data support the emerging concept that ribosome-dependent toxins have diverse modes of mRNA recognition.


    Organizational Affiliation

    Emory University School of Medicine, Department of Biochemistry, 1510 Clifton Road NE, Atlanta, GA 30322, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endoribonuclease HigB
A
117Proteus vulgarisMutation(s): 0 
Gene Names: higB
EC: 3.1.-.-
Find proteins for Q7A225 (Proteus vulgaris)
Go to UniProtKB:  Q7A225
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.101 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.138 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 55.776α = 90.00
b = 33.166β = 115.49
c = 51.492γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-10-05
    Type: Database references