2AH2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.099 
  • R-Value Observed: 0.099 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


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

  • DOI: https://doi.org/10.1016/j.str.2004.02.036
  • Primary Citation of 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
trans-sialidase648Trypanosoma cruziMutation(s): 7 
EC: 3.2.1.18
UniProt
Find proteins for Q26966 (Trypanosoma cruzi)
Explore Q26966 
Go to UniProtKB:  Q26966
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ26966
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FSI
Query on FSI

Download Ideal Coordinates CCD File 
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
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
IPA
Query on IPA

Download Ideal Coordinates CCD File 
G [auth A]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.099 
  • R-Value Observed: 0.099 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.149α = 90
b = 128.69β = 108.74
c = 54.298γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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