1S0J | pdb_00001s0j

Trypanosoma cruzi trans-sialidase in complex with MuNANA (Michaelis complex)

• PDB DOI: https://doi.org/10.2210/pdb1S0J/pdb

• Classification: HYDROLASE
• Organism(s): Trypanosoma cruzi
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-12-31 Released: 2004-05-18 
• Deposition Author(s): Amaya, M.F., Watts, A.G., Damager, I., Wehenkel, A., Nguyen, T., Buschiazzo, A., Paris, G., Frasch, A.C., Withers, S.G., Alzari, P.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.194 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.162 (Depositor) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Structural Insights into the Catalytic Mechanism of Trypanosoma cruzi trans-Sialidase.

Amaya, M.F., Watts, A.G., Damager, I., Wehenkel, A., Nguyen, T., Buschiazzo, A., Paris, G., Frasch, A.C., Withers, S.G., Alzari, P.M.

(2004) Structure 12: 775-784

• PubMed: 15130470 
• DOI: https://doi.org/10.1016/j.str.2004.02.036
• Primary Citation Related Structures: 
  1S0I, 1S0J, 2AH2


• PubMed Abstract: 
  

  Sialidases are a superfamily of sialic-acid-releasing enzymes that are of significant interest due to their implication as virulence factors in the pathogenesis of a number of diseases. However, extensive studies of viral and microbial sialidases have failed to provide a comprehensive picture of their mechanistic properties, in part because the structures of competent enzyme-substrate complexes and reaction intermediates have never been described. Here we report these structures for the Trypanosoma cruzi trans-sialidase (TcTS), showing that catalysis by sialidases occurs via a similar mechanism to that of other retaining glycosidases, but with some intriguing differences that may have evolved in response to the substrate structure.

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Organizational Affiliation: 
• Unité de Biochimie Structurale, CNRS URA 2185, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 71.81 kDa 
• Atom Count: 5,450 
• Modeled Residue Count: 623 
• Deposited Residue Count: 648 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
trans-sialidase	A	648	Trypanosoma cruzi	Mutation(s): 8  EC: 3.2.1.18
UniProt
Find proteins for Q26966 (Trypanosoma cruzi) Explore Q26966  Go to UniProtKB:  Q26966

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MUS	B [auth A]	4-METHYL-2-OXO-2H-CHROMEN-7-YL 5-(ACETYLAMINO)-3,5-DIDEOXY-L-ERYTHRO-NON-2-ULOPYRANOSIDONIC ACID C21 H25 N O11 KKDWIUJBUSOPGC-GKHMPSLRSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.194 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.162 (Depositor) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.373	α = 90
b = 129.423	β = 108.33
c = 54.234	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-18 
Deposition Author(s): Amaya, M.F., Watts, A.G., Damager, I., Wehenkel, A., Nguyen, T., Buschiazzo, A., Paris, G., Frasch, A.C., Withers, S.G., Alzari, P.M.

Revision History  

• Version 1.0: 2004-05-18
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-23
  Changes: Data collection, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary