Ruminococcus gnavus GH29 fucosidase E1_10125 in complex with fucose

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Fucosidases from the human gut symbiont Ruminococcus gnavus.

Wu, H.Rebello, O.Crost, E.H.Owen, C.D.Walpole, S.Bennati-Granier, C.Ndeh, D.Monaco, S.Hicks, T.Colvile, A.Urbanowicz, P.A.Walsh, M.A.Angulo, J.Spencer, D.I.R.Juge, N.

(2021) Cell Mol Life Sci 78: 675-693

  • DOI: https://doi.org/10.1007/s00018-020-03514-x
  • Primary Citation of Related Structures:  
    6TR3, 6TR4

  • PubMed Abstract: 

    The availability and repartition of fucosylated glycans within the gastrointestinal tract contributes to the adaptation of gut bacteria species to ecological niches. To access this source of nutrients, gut bacteria encode α-L-fucosidases (fucosidases) which catalyze the hydrolysis of terminal α-L-fucosidic linkages. We determined the substrate and linkage specificities of fucosidases from the human gut symbiont Ruminococcus gnavus. Sequence similarity network identified strain-specific fucosidases in R. gnavus ATCC 29149 and E1 strains that were further validated enzymatically against a range of defined oligosaccharides and glycoconjugates. Using a combination of glycan microarrays, mass spectrometry, isothermal titration calorimetry, crystallographic and saturation transfer difference NMR approaches, we identified a fucosidase with the capacity to recognize sialic acid-terminated fucosylated glycans (sialyl Lewis X/A epitopes) and hydrolyze α1-3/4 fucosyl linkages in these substrates without the need to remove sialic acid. Molecular dynamics simulation and docking showed that 3'-Sialyl Lewis X (sLeX) could be accommodated within the binding site of the enzyme. This specificity may contribute to the adaptation of R. gnavus strains to the infant and adult gut and has potential applications in diagnostic glycomic assays for diabetes and certain cancers.

  • Organizational Affiliation

    The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
F5/8 type C domain-containing protein552Mediterraneibacter gnavus E1Mutation(s): 0 
Find proteins for A0A6N3BKT0 (Mediterraneibacter gnavus)
Explore A0A6N3BKT0 
Go to UniProtKB:  A0A6N3BKT0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6N3BKT0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.219α = 90
b = 48.643β = 115.02
c = 80.287γ = 90
Software Package:
Software NamePurpose
xia2data scaling
PDB_EXTRACTdata extraction
DIALSdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M029042
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/J004529/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-28
    Type: Initial release
  • Version 1.1: 2021-02-17
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description