6T2S

Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.199 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown.

Crouch, L.I.Liberato, M.V.Urbanowicz, P.A.Basle, A.Lamb, C.A.Stewart, C.J.Cooke, K.Doona, M.Needham, S.Brady, R.R.Berrington, J.E.Madunic, K.Wuhrer, M.Chater, P.Pearson, J.P.Glowacki, R.Martens, E.C.Zhang, F.Linhardt, R.J.Spencer, D.I.R.Bolam, D.N.

(2020) Nat Commun 11: 4017-4017

  • DOI: https://doi.org/10.1038/s41467-020-17847-5
  • Primary Citation of Related Structures:  
    6T2N, 6T2O, 6T2P, 6T2Q, 6T2R, 6T2S

  • PubMed Abstract: 

    The thick mucus layer of the gut provides a barrier to infiltration of the underlying epithelia by both the normal microbiota and enteric pathogens. Some members of the microbiota utilise mucin glycoproteins as a nutrient source, but a detailed understanding of the mechanisms used to breakdown these complex macromolecules is lacking. Here we describe the discovery and characterisation of endo-acting enzymes from prominent mucin-degrading bacteria that target the polyLacNAc structures within oligosaccharide side chains of both animal and human mucins. These O-glycanases are part of the large and diverse glycoside hydrolase 16 (GH16) family and are often lipoproteins, indicating that they are surface located and thus likely involved in the initial step in mucin breakdown. These data provide a significant advance in our knowledge of the mechanism of mucin breakdown by the normal microbiota. Furthermore, we also demonstrate the potential use of these enzymes as tools to explore changes in O-glycan structure in a number of intestinal disease states.


  • Organizational Affiliation

    Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK. l.i.crouch@bham.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoside hydrolase family 16 proteinA [auth AAA],
B [auth BBB],
C [auth CCC]
241Bacteroides finegoldii DSM 17565Mutation(s): 0 
Gene Names: DXB57_07550
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranoseD [auth A],
E [auth B],
F [auth C]
3N/A
Glycosylation Resources
GlyTouCan:  G06580KR
GlyCosmos:  G06580KR
GlyGen:  G06580KR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.199 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.62α = 90
b = 156.62β = 90
c = 197.051γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
GDAdata collection
Aimlessdata scaling
PHASERphasing
Cootmodel building
DIALSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M029018/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2020-08-26
    Changes: Database references, Structure summary
  • Version 2.2: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary