8OW8 | pdb_00008ow8

Crystal Structure of the Catalytic Domain of a Botulinum Neurotoxin Homologue from Enterococcus faecium

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.224 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.189 (DCC) 

Starting Model: in silico
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This is version 1.1 of the entry. See complete history. 

Literature

Crystal Structure of the Catalytic Domain of a Botulinum Neurotoxin Homologue from Enterococcus faecium : Potential Insights into Substrate Recognition.

Gregory, K.S., Hall, P.R., Onuh, J.P., Mojanaga, O.O., Liu, S.M., Acharya, K.R.

(2023) Int J Mol Sci 24

  • DOI: https://doi.org/10.3390/ijms241612721
  • Primary Citation Related Structures: 
    8OW8

  • PubMed Abstract: 

    Clostridium botulinum neurotoxins (BoNTs) are the most potent toxins known, causing the deadly disease botulism. They function through Zn 2+ -dependent endopeptidase cleavage of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, preventing vesicular fusion and subsequent neurotransmitter release from motor neurons. Several serotypes of BoNTs produced by Clostridium botulinum (BoNT/A-/G and/X) have been well-characterised over the years. However, a BoNT-like gene (homologue of BoNT) was recently identified in the non-clostridial species, Enterococcus faecium, which is the leading cause of hospital-acquired multi-drug resistant infections. Here, we report the crystal structure of the catalytic domain of a BoNT homologue from Enterococcus faecium (LC/En) at 2.0 Å resolution. Detailed structural analysis in comparison with the full-length BoNT/En AlphaFold2-predicted structure, LC/A (from BoNT/A), and LC/F (from BoNT/F) revealed putative subsites and exosites (including loops 1-5) involved in recognition of LC/En substrates. LC/En also appears to possess a conserved autoproteolytic cleavage site whose function is yet to be established.

    • Organizational Affiliation: 
    • Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK.

Macromolecule Content 

  • Total Structure Weight: 51.21 kDa 
  • Atom Count: 3,407 
  • Modeled Residue Count: 401 
  • Deposited Residue Count: 446 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Botulinum-like toxin eBoNT/J light chain446EnterococcusMutation(s): 0 
Gene Names: A5816_002916
EC: 3.4.24.69
UniProt
Find proteins for A0A242DI27 (Enterococcus sp. (strain 3G1_DIV0629))
Explore A0A242DI27 
Go to UniProtKB:  A0A242DI27
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A242DI27
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.224 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.189 (DCC) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.894α = 90
b = 143.894β = 90
c = 51.695γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2023-09-06
    Changes: Database references