1YXW | pdb_00001yxw

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

• PDB DOI: https://doi.org/10.2210/pdb1YXW/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium tetani
• Mutation(s): No 


• Deposited: 2005-02-22 Released: 2005-03-15 
• Deposition Author(s): Jayaraman, S., Eswaramoorthy, S., Kumaran, D., Swaminathan, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.274 (Depositor) 
• R-Value Work: 
  0.224 (Depositor) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

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

• PubMed: 16104015 
• DOI: https://doi.org/10.1002/prot.20595
• Primary Citation Related Structures: 
  1YXW, 1YYN


• 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-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.

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Organizational Affiliation: 
• Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 51.01 kDa 
• Atom Count: 3,802 
• Modeled Residue Count: 441 
• Deposited Residue Count: 441 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetanus toxin (Tentoxylysin)	A	441	Clostridium tetani	Mutation(s): 0  EC: 3.4.24.68
UniProt
Find proteins for P04958 (Clostridium tetani (strain Massachusetts / E88)) Explore P04958  Go to UniProtKB:  P04958

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRP	D [auth A]	TRYPTOPHAN C11 H12 N2 O2 QIVBCDIJIAJPQS-VIFPVBQESA-N
TYR	B [auth A]	TYROSINE C9 H11 N O3 OUYCCCASQSFEME-QMMMGPOBSA-N
GLU	C [auth A]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.274 (Depositor) 
• R-Value Work:  0.224 (Depositor) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.757	α = 90
b = 79.183	β = 90
c = 90.265	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-15 
Deposition Author(s): Jayaraman, S., Eswaramoorthy, S., Kumaran, D., Swaminathan, S.

Revision History  

• Version 1.0: 2005-03-15
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description