5F7W

Blood group antigen binding adhesin BabA of Helicobacter pylori strain 17875 in complex with blood group B Lewis b heptasaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Insights into Polymorphic ABO Glycan Binding by Helicobacter pylori.

Moonens, K.Gideonsson, P.Subedi, S.Bugaytsova, J.Romao, E.Mendez, M.Norden, J.Fallah, M.Rakhimova, L.Shevtsova, A.Lahmann, M.Castaldo, G.Brannstrom, K.Coppens, F.Lo, A.W.Ny, T.Solnick, J.V.Vandenbussche, G.Oscarson, S.Hammarstrom, L.Arnqvist, A.Berg, D.E.Muyldermans, S.Boren, T.Remaut, H.

(2016) Cell Host Microbe 19: 55-66

  • DOI: 10.1016/j.chom.2015.12.004
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Helicobacter pylori adhesin BabA binds mucosal ABO/Le(b) blood group (bg) carbohydrates. BabA facilitates bacterial attachment to gastric surfaces, increasing strain virulence and forming a recognized risk factor for peptic ulcers and gastric can ...

    The Helicobacter pylori adhesin BabA binds mucosal ABO/Le(b) blood group (bg) carbohydrates. BabA facilitates bacterial attachment to gastric surfaces, increasing strain virulence and forming a recognized risk factor for peptic ulcers and gastric cancer. High sequence variation causes BabA functional diversity, but the underlying structural-molecular determinants are unknown. We generated X-ray structures of representative BabA isoforms that reveal a polymorphic, three-pronged Le(b) binding site. Two diversity loops, DL1 and DL2, provide adaptive control to binding affinity, notably ABO versus O bg preference. H. pylori strains can switch bg preference with single DL1 amino acid substitutions, and can coexpress functionally divergent BabA isoforms. The anchor point for receptor binding is the embrace of an ABO fucose residue by a disulfide-clasped loop, which is inactivated by reduction. Treatment with the redox-active pharmaceutic N-acetylcysteine lowers gastric mucosal neutrophil infiltration in H. pylori-infected Le(b)-expressing mice, providing perspectives on possible H. pylori eradication therapies.


    Organizational Affiliation

    Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adhesin binding fucosylated histo-blood group antigen
A, B
466Helicobacter pyloriMutation(s): 0 
Gene Names: babA2
Find proteins for O52269 (Helicobacter pylori)
Go to UniProtKB:  O52269
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nanobody Nb-ER19
C, D
120N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download SDF File 
Download CCD File 
A, B
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
A, B
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GLA
Query on GLA

Download SDF File 
Download CCD File 
A, B
ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.090α = 90.00
b = 132.440β = 94.93
c = 123.510γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Flanders Institute of Biotechnology (VIB)BelgiumPRJ9
Flanders Science Foundation (FWO)BelgiumOdysseus program
Hercules FoundationBelgiumUABR/09/005
Vetenskapsradet/VRSweden--
CancerfondenSweden--

Revision History 

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-01-27
    Type: Database references