1MS0 | pdb_00001ms0

Monoclinic form of Trypanosoma cruzi trans-sialidase, in complex with 3-deoxy-2,3-dehydro-N-acetylneuraminic acid (DANA)and lactose

• PDB DOI: https://doi.org/10.2210/pdb1MS0/pdb

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


• Deposited: 2002-09-19 Released: 2003-03-25 
• Deposition Author(s): Buschiazzo, A., Amaya, M.F., Cremona, M.L., Frasch, A.C., Alzari, P.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.253 (Depositor) 
• R-Value Work: 
  0.191 (Depositor) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

The crystal structure and mode of action of trans-sialidase, a key enzyme in Trypanosoma cruzi pathogenesis

Buschiazzo, A., Amaya, M.F., Cremona, M.L., Frasch, A.C., Alzari, P.M.

(2002) Mol Cell 10: 757-768

• PubMed: 12419220 
• DOI: https://doi.org/10.1016/s1097-2765(02)00680-9
• Primary Citation Related Structures: 
  1MR5, 1MS0, 1MS1, 1MS3, 1MS4, 1MS5, 1MS8, 1MS9


• PubMed Abstract: 
  

  Trans-sialidases (TS) are GPI-anchored surface enzymes expressed in specific developmental stages of trypanosome parasites like Trypanosoma cruzi, the etiologic agent of Chagas disease, and T. brucei, the causative agent of sleeping sickness. TS catalyzes the transfer of sialic acid residues from host to parasite glycoconjugates through a transglycosidase reaction that appears to be critical for T. cruzi survival and cell invasion capability. We report here the structure of the T. cruzi trans-sialidase, alone and in complex with sugar ligands. Sialic acid binding is shown to trigger a conformational switch that modulates the affinity for the acceptor substrate and concomitantly creates the conditions for efficient transglycosylation. The structure provides a framework for the structure-based design of novel inhibitors with potential therapeutic applications.

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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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 144.05 kDa 
• Atom Count: 10,372 
• Modeled Residue Count: 1,246 
• Deposited Residue Count: 1,296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
trans-sialidase	A, B	648	Trypanosoma cruzi	Mutation(s): 7  EC: 3.2.1.18
UniProt
Find proteins for Q26966 (Trypanosoma cruzi) Explore Q26966  Go to UniProtKB:  Q26966

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan: G84224TW GlyCosmos: G84224TW GlyGen: G84224TW

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DAN	E [auth A], F [auth B]	2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID C11 H17 N O8 JINJZWSZQKHCIP-UFGQHTETSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004	C, D	beta-lactose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.253 (Depositor) 
• R-Value Work:  0.191 (Depositor) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.222	α = 90
b = 133.374	β = 91.41
c = 90.606	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-25 
Deposition Author(s): Buschiazzo, A., Amaya, M.F., Cremona, M.L., Frasch, A.C., Alzari, P.M.

Revision History  

• Version 1.0: 2003-03-25
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-02-01
  Changes: Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2021-10-27
  Changes: Database references, Structure summary
• Version 3.0: 2024-12-25
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary