2AH2 | pdb_00002ah2

Trypanosoma cruzi trans-sialidase in complex with 2,3-difluorosialic acid (covalent intermediate)

• PDB DOI: https://doi.org/10.2210/pdb2AH2/pdb
• Entry: 2AH2 supersedes: 1S0K

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


• Deposited: 2005-07-27 Released: 2005-08-23 
• 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: 1.60 Å
• R-Value Free: 
  0.152 (Depositor), 0.152 (DCC) 
• R-Value Work: 
  0.099 (Depositor), 0.100 (DCC) 
• R-Value Observed: 
  0.099 (Depositor) 

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: 72.09 kDa 
• Atom Count: 5,871 
• Modeled Residue Count: 624 
• 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): 7  EC: 3.2.1.18
UniProt
Find proteins for Q26966 (Trypanosoma cruzi) Explore Q26966  Go to UniProtKB:  Q26966

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FSI	C [auth A]	5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid C11 H18 F N O9 ALJLGESFXXDPKH-RISWTRDCSA-N
GOL	D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IPA	G [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.152 (Depositor), 0.152 (DCC) 
• R-Value Work:  0.099 (Depositor), 0.100 (DCC) 
• R-Value Observed: 0.099 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.149	α = 90
b = 128.69	β = 108.74
c = 54.298	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-23 
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.
• This entry supersedes: 1S0K

Revision History  

• Version 1.0: 2005-08-23
  Type: Initial release
  
• Version 1.1: 2008-04-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.5: 2021-10-20
  Changes: Database references, Structure summary
• Version 1.6: 2024-11-13
  Changes: Data collection, Structure summary