6RIM

Crystal structure of the catalytic domain of the Weissela oryzae botulinum like toxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the catalytic domain of the Weissella oryzae botulinum-like toxin.

Kosenina, S.Masuyer, G.Zhang, S.Dong, M.Stenmark, P.

(2019) Febs Lett. 593: 1403-1410

  • DOI: 10.1002/1873-3468.13446

  • PubMed Abstract: 
  • Botulinum neurotoxins (BoNTs) are the most potent toxins known. So far, eight serotypes have been identified that all act as zinc-dependent endopeptidases targeting SNARE proteins and inhibiting the release of neurotransmitters. Recently, the first b ...

    Botulinum neurotoxins (BoNTs) are the most potent toxins known. So far, eight serotypes have been identified that all act as zinc-dependent endopeptidases targeting SNARE proteins and inhibiting the release of neurotransmitters. Recently, the first botulinum toxin-like protein was identified outside the Clostridial genus, designated BoNT/Wo in the genome of Weissella oryzae. Here, we report the 1.6 Å X-ray crystal structure of the light chain of BoNT/Wo (LC/Wo). LC/Wo presents the core fold common to BoNTs but has an unusually wide, open and negatively charged catalytic pocket, with an additional Ca 2+ ion besides the zinc ion and a unique ß-hairpin motif. The structural information will help establish the substrate profile of BoNT/Wo and help our understanding of how BoNT evolved.


    Organizational Affiliation

    Department of Urology, Boston Children's Hospital, Boston, MA, USA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA.,Department of Biochemistry and Biophysics, Stockholm University, Sweden.,Department of Experimental Medical Science, Lund University, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative botulinum-like toxin Wo
A, B, C, D, E, F, G, H
498Weissella oryzae (strain DSM 25784 / JCM 18191 / SG25)Mutation(s): 0 
EC: 3.4.24.69
Find proteins for A0A069CUU9 (Weissella oryzae (strain DSM 25784 / JCM 18191 / SG25))
Go to UniProtKB:  A0A069CUU9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.151 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 57.908α = 101.71
b = 105.208β = 90.00
c = 179.621γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2018-03406

Revision History 

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-06-05
    Type: Data collection, Derived calculations
  • Version 1.2: 2019-07-03
    Type: Data collection, Database references
  • Version 1.3: 2019-08-21
    Type: Data collection