6ER2

Ruminococcus gnavus IT-sialidase CBM40


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Unravelling the specificity and mechanism of sialic acid recognition by the gut symbiont Ruminococcus gnavus.

Owen, C.D.Tailford, L.E.Monaco, S.Suligoj, T.Vaux, L.Lallement, R.Khedri, Z.Yu, H.Lecointe, K.Walshaw, J.Tribolo, S.Horrex, M.Bell, A.Chen, X.Taylor, G.L.Varki, A.Angulo, J.Juge, N.

(2017) Nat Commun 8: 2196-2196

  • DOI: 10.1038/s41467-017-02109-8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ruminococcus gnavus is a human gut symbiont wherein the ability to degrade mucins is mediated by an intramolecular trans-sialidase (RgNanH). RgNanH comprises a GH33 catalytic domain and a sialic acid-binding carbohydrate-binding module (CBM40). Here ...

    Ruminococcus gnavus is a human gut symbiont wherein the ability to degrade mucins is mediated by an intramolecular trans-sialidase (RgNanH). RgNanH comprises a GH33 catalytic domain and a sialic acid-binding carbohydrate-binding module (CBM40). Here we used glycan arrays, STD NMR, X-ray crystallography, mutagenesis and binding assays to determine the structure and function of RgNanH_CBM40 (RgCBM40). RgCBM40 displays the canonical CBM40 β-sandwich fold and broad specificity towards sialoglycans with millimolar binding affinity towards α2,3- or α2,6-sialyllactose. RgCBM40 binds to mucus produced by goblet cells and to purified mucins, providing direct evidence for a CBM40 as a novel bacterial mucus adhesin. Bioinformatics data show that RgCBM40 canonical type domains are widespread among Firmicutes. Furthermore, binding of R. gnavus ATCC 29149 to intestinal mucus is sialic acid mediated. Together, this study reveals novel features of CBMs which may contribute to the biogeography of symbiotic bacteria in the gut.


    Organizational Affiliation

    School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Glycobiology Research and Training Center (GRTC), Departments of Medicine and Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093-0687, USA.,Department of Chemistry, University of California-Davis, Davis, CA, 95616, USA.,The Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA, UK.,Biomolecular Sciences Building, University of St Andrews, St Andrews, KY16 9ST, UK.,Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK.,School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.,Ajinomoto Althea Inc, 11040 Roselle Street, San Diego, CA, 92121, USA.,The Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA, UK. nathalie.juge@quadram.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BNR/Asp-box repeat protein
A, B
190Ruminococcus gnavus (strain ATCC 29149 / VPI C7-9)Mutation(s): 0 
Find proteins for A7B557 (Ruminococcus gnavus (strain ATCC 29149 / VPI C7-9))
Go to UniProtKB:  A7B557
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.683α = 90.00
b = 72.745β = 104.94
c = 51.292γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data reduction
DENZOdata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/F016778/1

Revision History 

  • Version 1.0: 2018-05-02
    Type: Initial release