3DWQ

Crystal structure of the A-subunit of the AB5 toxin from E. coli with Neu5Gc-2,3Gal-1,3GlcNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

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
  • Structures With Same Primary Citation

  • 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: subBC9098_24495C9Z37_27580C9Z78_25705LH0182
Find proteins for Q3ZTX8 (Escherichia coli)
Go to UniProtKB:  Q3ZTX8
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NGC
Query on NGC

Download CCD File 
A, C, D, E
3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid
C11 H19 N O10
FDJKUWYYUZCUJX-VTERZIIISA-N
 Ligand Interaction
1PE
Query on 1PE

Download CCD File 
A, B, D, E
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
NGA
Query on NGA

Download CCD File 
A, C, D, E
N-ACETYL-D-GALACTOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-JAJWTYFOSA-N
 Ligand Interaction
GAL
Query on GAL

Download CCD File 
A, C, D, E
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
POL
Query on POL

Download CCD File 
A, C, D, E
N-PROPANOL
C3 H8 O
BDERNNFJNOPAEC-UHFFFAOYSA-N
 Ligand Interaction
AZI
Query on AZI

Download CCD File 
A, C, D, E
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.253α = 90
b = 97.253β = 90
c = 163.52γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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