1YYN

A common binding site for disialyllactose and a tri-peptide in the C-fragment of tetanus neurotoxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Common binding site for disialyllactose and tri-peptide in C-fragment of tetanus neurotoxin

Jayaraman, S.Eswaramoorthy, S.Kumaran, D.Swaminathan, S.

(2005) Proteins 61: 288-295

  • DOI: 10.1002/prot.20595
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Clostridial neurotoxins are comprised of botulinum (BoNT) and tetanus (TeNT), which share significant structural and functional similarity. Crystal structures of the binding domain of TeNT complexed with disialyllactose (DiSia) and a tri-peptide Tyr- ...

    Clostridial neurotoxins are comprised of botulinum (BoNT) and tetanus (TeNT), which share significant structural and functional similarity. Crystal structures of the binding domain of TeNT complexed with disialyllactose (DiSia) and a tri-peptide Tyr-Glu-Trp (YEW) have been determined to 2.3 and 2.2 A, respectively. Both DiSia and YEW bind in a shallow cleft region on the surface of the molecule in the beta-trefoil domain, interacting with a set of common residues, Asp1147, Asp1214, Asn1216, and Arg1226. DiSia and YEW binding at the same site in tetanus toxin provides a putative site that could be occupied either by a ganglioside moiety or a peptide. Soaking experiments with a mixture of YEW and DiSia show that YEW competes with DiSia, suggesting that YEW can be used to block ganglioside binding. A comparison with the TeNT binding domain in complex with small molecules, BoNT/A and /B, provides insight into the different modes of ganglioside binding.


    Organizational Affiliation

    Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tetanus toxin
A
441Clostridium tetani (strain Massachusetts / E88)Mutation(s): 0 
Gene Names: tetX
EC: 3.4.24.68
Find proteins for P04958 (Clostridium tetani (strain Massachusetts / E88))
Go to UniProtKB:  P04958
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download SDF File 
Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
GLA
Query on GLA

Download SDF File 
Download CCD File 
A
ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
 Ligand Interaction
SIA
Query on SIA

Download SDF File 
Download CCD File 
A
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.255 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.907α = 90.00
b = 78.930β = 90.00
c = 90.977γ = 90.00
Software Package:
Software NamePurpose
CBASSdata collection
HKL-2000data scaling
CNSrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-15
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance