3F5E

Crystal structure of Toxoplasma gondii micronemal protein 1 bound to 2'F-3'SiaLacNAc1-3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Detailed insights from microarray and crystallographic studies into carbohydrate recognition by microneme protein 1 (MIC1) of Toxoplasma gondii.

Garnett, J.A.Liu, Y.Leon, E.Allman, S.A.Friedrich, N.Saouros, S.Curry, S.Soldati-Favre, D.Davis, B.G.Feizi, T.Matthews, S.

(2009) Protein Sci. 18: 1935-1947

  • DOI: 10.1002/pro.204
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The intracellular protozoan Toxoplasma gondii is among the most widespread parasites. The broad host cell range of the parasite can be explained by carbohydrate microarray screening analyses that have demonstrated the ability of the T. gondii adhesiv ...

    The intracellular protozoan Toxoplasma gondii is among the most widespread parasites. The broad host cell range of the parasite can be explained by carbohydrate microarray screening analyses that have demonstrated the ability of the T. gondii adhesive protein, TgMIC1, to bind to a wide spectrum of sialyl oligosaccharide ligands. Here, we investigate by further microarray analyses in a dose-response format the differential binding of TgMIC1 to 2-3- and 2-6-linked sialyl carbohydrates. Interestingly, two novel synthetic fluorinated analogs of 3'SiaLacNAc(1-4) and 3'SiaLacNAc(1-3) were identified as highly potent ligands. To understand the structural basis of the carbohydrate binding specificity of TgMIC1, we have determined the crystal structures of TgMIC1 micronemal adhesive repeat (MAR)-region (TgMIC1-MARR) in complex with five sialyl-N-acetyllactosamine analogs. These crystal structures have revealed a specific, water-mediated hydrogen bond network that accounts for the preferential binding of TgMIC1-MARR to arrayed 2-3-linked sialyl oligosaccharides and the high potency of the fluorinated analogs. Furthermore, we provide strong evidence for the first observation of a C--F...H--O hydrogen bond within a lectin-carbohydrate complex. Finally, detailed comparison with other oligosaccharide-protein complexes in the Protein Data Bank (PDB) reveals a new family of sialic-acid binding sites from lectins in parasites, bacteria, and viruses.


    Related Citations: 
    • Atomic resolution insight into host cell recognition by Toxoplasma gondii.
      Blumenschein, T.M.,Friedrich, N.,Childs, R.A.,Saouros, S.,Carpenter, E.P.,Campanero-Rhodes, M.A.,Simpson, P.,Chai, W.,Koutroukides, T.,Blackman, M.J.,Feizi, T.,Soldati-Favre, D.,Matthews, S.
      (2007) Embo J. 26: 2808


    Organizational Affiliation

    Division of Molecular Biosciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW72AZ, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Micronemal protein 1
A
246Toxoplasma gondiiMutation(s): 0 
Gene Names: MIC1
Find proteins for O00834 (Toxoplasma gondii)
Go to UniProtKB:  O00834
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2FG
Query on 2FG

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Download CCD File 
A
2-FLUORO-2-DEOXY-BETA-D-GALACTOPYRANOSE
C6 H11 F O5
ZCXUVYAZINUVJD-VFUOTHLCSA-N
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SIA
Query on SIA

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Download CCD File 
A
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.165 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 66.325α = 90.00
b = 66.325β = 90.00
c = 172.091γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement
MAR345dtbdata collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.2: 2016-02-17
    Type: Derived calculations, Non-polymer description