4ELC

Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A C134 mutant with MTSEA modified Cys-165


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Framework for Covalent Inhibition of Clostridium botulinum Neurotoxin A by Targeting Cys165.

Stura, E.A.Le Roux, L.Guitot, K.Garcia, S.Bregant, S.Beau, F.Vera, L.Collet, G.Ptchelkine, D.Bakirci, H.Dive, V.

(2012) J.Biol.Chem. 287: 33607-33614

  • DOI: 10.1074/jbc.M112.396697
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Clostridium botulinum neurotoxin type A (BoNT/A) is one of the most potent toxins for humans and a major biothreat agent. Despite intense chemical efforts over the past 10 years to develop inhibitors of its catalytic domain (catBoNT/A), highly potent ...

    Clostridium botulinum neurotoxin type A (BoNT/A) is one of the most potent toxins for humans and a major biothreat agent. Despite intense chemical efforts over the past 10 years to develop inhibitors of its catalytic domain (catBoNT/A), highly potent and selective inhibitors are still lacking. Recently, small inhibitors were reported to covalently modify catBoNT/A by targeting Cys(165), a residue located in the enzyme active site just above the catalytic zinc ion. However, no direct proof of Cys(165) modification was reported, and the poor accessibility of this residue in the x-ray structure of catBoNT/A raises concerns about this proposal. To clarify this issue, the functional role of Cys(165) was first assessed through a combination of site-directed mutagenesis and structural studies. These data suggested that Cys(165) is more involved in enzyme catalysis rather than in structural property. Then by peptide mass fingerprinting and x-ray crystallography, we demonstrated that a small compound containing a sulfonyl group acts as inhibitor of catBoNT/A through covalent modification of Cys(165). The crystal structure of this covalent complex offers a structural framework for developing more potent covalent inhibitors catBoNT/A. Other zinc metalloproteases can be founded in the protein database with a cysteine at a similar location, some expressed by major human pathogens; thus this work should find broader applications for developing covalent inhibitors.


    Organizational Affiliation

    Commissariat à l'Energie Atomique, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines, CE-Saclay, 91191 Gif-sur-Yvette, Cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Botulinum neurotoxin A light chain
A
445Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A)Mutation(s): 1 
Gene Names: botA (bna)
Find proteins for P0DPI1 (Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A))
Go to UniProtKB:  P0DPI1
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
LI
Query on LI

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A
LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
LMR
Query on LMR

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A
(2S)-2-hydroxybutanedioic acid
L-Malate
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N
 Ligand Interaction
IMD
Query on IMD

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A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
DMS
Query on DMS

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A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

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A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
0QL
Query on 0QL
A
L-PEPTIDE LINKINGC5 H12 N2 O2 S2CYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0QLKi: 625000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.169 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 65.290α = 90.00
b = 65.290β = 90.00
c = 200.910γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XSCALEdata scaling
DNAdata collection
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2012-08-29
    Type: Database references
  • Version 1.2: 2012-10-17
    Type: Database references