5G3L

ESCHERICHIA COLI HEAT LABILE ENTEROTOXIN TYPE IIB B-PENTAMER COMPLEXED WITH SIALYLATED SUGAR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Biochemical and Structural Characterization of the Novel Sialic Acid-Binding Site of Escherichia Coli Heat-Labile Enterotoxin Lt-Iib.

Zalem, D.Ribeiro, J.P.Varrot, A.Lebens, M.Imberty, A.Teneberg, S.

(2016) Biochem.J. 473: 3923

  • DOI: 10.1042/BCJ20160575

  • PubMed Abstract: 
  • The structurally related AB <sub>5 </sub>-type heat-labile enterotoxins of Escherichia coli and Vibrio cholerae are classified into two major types. The type I group includes cholera toxin (CT) and E. coli LT-I, whereas the type II subfamily comprise ...

    The structurally related AB 5 -type heat-labile enterotoxins of Escherichia coli and Vibrio cholerae are classified into two major types. The type I group includes cholera toxin (CT) and E. coli LT-I, whereas the type II subfamily comprises LT-IIa, LT-IIb and LT-IIc. The carbohydrate-binding specificities of LT-IIa, LT-IIb and LT-IIc are distinctive from those of cholera toxin and E. coli LT-I. Whereas CT and LT-I bind primarily to the GM1 ganglioside, LT-IIa binds to gangliosides GD1a, GD1b and GM1, LT-IIb binds to the GD1a and GT1b gangliosides, and LT-IIc binds to GM1, GM2, GM3 and GD1a. These previous studies of the binding properties of type II B-subunits have been focused on ganglio core chain gangliosides. To further define the carbohydrate binding specificity of LT-IIb B-subunits, we have investigated its binding to a collection of gangliosides and non-acid glycosphingolipids with different core chains. A high-affinity binding of LT-IIb B-subunits to gangliosides with a neolacto core chain, such as Neu5Gcα3- and Neu5Acα3-neolactohexaosylceramide, and Neu5Gcα3- and Neu5Acα3-neolactooctaosylceramide was detected. An LT-IIb-binding ganglioside was isolated from human small intestine and characterized as Neu5Acα3-neolactohexaosylceramide. The crystal structure of the B-subunit of LT-IIb with the pentasaccharide moiety of Neu5Acα3-neolactotetraosylceramide (Neu5Ac-nLT: Neu5Acα3Galβ4GlcNAcβ3Galβ4Glc) was determined providing the first information for a sialic-binding site in this subfamily, with clear differences from that of CT and LT-I.


    Organizational Affiliation

    Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, The Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden.,Centre de Recherches sur les Macromolécules Végétales (UPR5301, CNRS and University Grenoble Alpes), BP53, F-38041 Grenoble Cedex 09, France.,Institute of Biomedicine, Department of Medical Microbiology and Immunology, The Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEAT-LABILE ENTEROTOXIN IIB, B CHAIN
D, E, H
99Escherichia coliMutation(s): 0 
Find proteins for P43529 (Escherichia coli)
Go to UniProtKB:  P43529
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HEAT-LABILE ENTEROTOXIN IIB, B CHAIN
F, G
99Escherichia coliMutation(s): 0 
Find proteins for P43529 (Escherichia coli)
Go to UniProtKB:  P43529
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
D, E, G, H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
D, G, H
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
SIA
Query on SIA

Download SDF File 
Download CCD File 
D, E, G, H
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ME0
Query on ME0
D, E, H
L-peptide linkingC5 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.564α = 90.00
b = 68.015β = 90.00
c = 154.513γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-11-09
    Type: Database references