3DWA

Crystal structure of the B-subunit of the AB5 toxin from E. coli

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.084 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Incorporation of a non-human glycan mediates human susceptibility to a bacterial toxin

Byres, E., Paton, A.W., Paton, J.C., Lofling, J.C., Smith, D.F., Wilce, M.C.J., Talbot, U.M., Chong, D.C., Yu, H., Huang, S., Chen, X., Varki, N.M., Varki, A., Rossjohn, J., Beddoe, T.

(2008) Nature 456: 648-652

  • DOI: 10.1038/nature07428
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • AB(5) toxins comprise an A subunit that corrupts essential eukaryotic cell functions, and pentameric B subunits that direct target-cell uptake after binding surface glycans. Subtilase cytotoxin (SubAB) is an AB(5) toxin secreted by Shiga toxigenic Es ...

    AB(5) toxins comprise an A subunit that corrupts essential eukaryotic cell functions, and pentameric B subunits that direct target-cell uptake after binding surface glycans. Subtilase cytotoxin (SubAB) is an AB(5) toxin secreted by Shiga toxigenic Escherichia coli (STEC), which causes serious gastrointestinal disease in humans. SubAB causes haemolytic uraemic syndrome-like pathology in mice through SubA-mediated cleavage of BiP/GRP78, an essential endoplasmic reticulum chaperone. Here we show that SubB has a strong preference for glycans terminating in the sialic acid N-glycolylneuraminic acid (Neu5Gc), a monosaccharide not synthesized in humans. Structures of SubB-Neu5Gc complexes revealed the basis for this specificity, and mutagenesis of key SubB residues abrogated in vitro glycan recognition, cell binding and cytotoxicity. SubAB specificity for Neu5Gc was confirmed using mouse tissues with a human-like deficiency of Neu5Gc and human cell lines fed with Neu5Gc. Despite lack of Neu5Gc biosynthesis in humans, assimilation of dietary Neu5Gc creates high-affinity receptors on human gut epithelia and kidney vasculature. This, and the lack of Neu5Gc-containing body fluid competitors in humans, confers susceptibility to the gastrointestinal and systemic toxicities of SubAB. Ironically, foods rich in Neu5Gc are the most common source of STEC contamination. Thus a bacterial toxin's receptor is generated by metabolic incorporation of an exogenous factor derived from food.

    Organizational Affiliation: 

    Protein Crystallography Unit and ARC Centre of Excellence for Structural and Functional Microbial Genomics, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Subtilase cytotoxin, subunit B
A, B, C, D, E
126Escherichia coliMutation(s): 0 
Gene Names: subB
Find proteins for Q3ZTX8 (Escherichia coli)
Go to UniProtKB:  Q3ZTX8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE
Download SDF File 
Download CCD File 
A, B, C, D, E
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.084 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 97.630α = 90.00
b = 97.630β = 90.00
c = 165.360γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance