1E1H

Crystal Structure of recombinant Botulinum Neurotoxin Type A Light Chain, self-inhibiting Zn endopeptidase.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

Crystal Structure of Clostridium Botulinum Neurotoxin Protease in a Product-Bound State: Evidence for Noncanonical Zinc Protease Activity

Segelke, B.W.Knapp, M.Kadhkodayan, S.Balhorn, R.Rupp, B.

(2004) Proc Natl Acad Sci U S A 101: 6888

  • DOI: https://doi.org/10.1073/pnas.0400584101
  • Primary Citation of Related Structures:  
    1E1H

  • PubMed Abstract: 

    Clostridium botulinum neurotoxins (BoNTs), the most potent toxins known, disrupt neurotransmission through proteolysis of proteins involved in neuroexocytosis. The light chains of BoNTs are unique zinc proteases that have stringent substrate specificity and require exceptionally long substrates. We have determined the crystal structure of the protease domain from BoNT serotype A (BoNT/A). The structure reveals a homodimer in a product-bound state, with loop F242-V257 from each monomer deeply buried in its partner's catalytic site. The loop, which acts as a substrate, is oriented in reverse of the canonical direction for other zinc proteases. The Y249-Y250 peptide bond of the substrate loop is hydrolyzed, leaving the Y249 product carboxylate coordinated to the catalytic zinc. From the crystal structure of the BoNT/A protease, detailed models of noncanonical binding and proteolysis can be derived which we propose are also consistent with BoNT/A binding and proteolysis of natural substrate synaptosome-associated protein of 25 kDa (SNAP-25). The proposed BoNT/A substrate-binding mode and catalytic mechanism are markedly different from those previously proposed for the BoNT serotype B.


  • Organizational Affiliation

    University of California, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94551, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BOTULINUM NEUROTOXIN TYPE A LIGHT CHAIN
A, C
287Clostridium botulinumMutation(s): 0 
EC: 3.4.24.69
UniProt
Find proteins for Q45894 (Clostridium botulinum (strain Kyoto / Type A2))
Explore Q45894 
Go to UniProtKB:  Q45894
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ45894
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BOTULINUM NEUROTOXIN TYPE A LIGHT CHAIN
B, D
174Clostridium botulinumMutation(s): 0 
EC: 3.4.24.69
UniProt
Find proteins for Q45894 (Clostridium botulinum (strain Kyoto / Type A2))
Explore Q45894 
Go to UniProtKB:  Q45894
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ45894
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.064α = 90
b = 94.263β = 103.52
c = 100.156γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-04-10
    Changes: Data collection, Other, Source and taxonomy
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2023-12-06
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description