Structure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-isofagomine and alpha- 1,2-mannobiose

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.112 
  • R-Value Observed: 0.113 

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This is version 2.0 of the entry. See complete history


Human Gut Bacteroidetes Can Utilize Yeast Mannan Through a Selfish Mechanism.

Cuskin, F.Lowe, E.C.Temple, M.Zhu, Y.Cameron, E.A.Pudlo, N.A.Porter, N.T.Urs, K.Thompson, A.J.Cartmell, A.Rogowski, A.Hamilton, B.S.Chen, R.Tolbert, T.J.Piens, K.Bracke, D.Vervecken, W.Hakki, Z.Speciale, G.Munoz-Munoz, J.L.Day, A.Pena, M.J.Mclean, R.Suits, M.D.L.Boraston, A.B.Atherly, T.Ziemer, C.J.Williams, S.J.Davies, G.J.Abbott, W.D.Martens, E.C.Gilbert, H.J.

(2015) Nature 517: 165

  • DOI: https://doi.org/10.1038/nature13995
  • Primary Citation of Related Structures:  
    4C1R, 4C1S, 4UTF

  • PubMed Abstract: 

    Yeasts, which have been a component of the human diet for at least 7,000 years, possess an elaborate cell wall α-mannan. The influence of yeast mannan on the ecology of the human microbiota is unknown. Here we show that yeast α-mannan is a viable food source for the Gram-negative bacterium Bacteroides thetaiotaomicron, a dominant member of the microbiota. Detailed biochemical analysis and targeted gene disruption studies support a model whereby limited cleavage of α-mannan on the surface generates large oligosaccharides that are subsequently depolymerized to mannose by the action of periplasmic enzymes. Co-culturing studies showed that metabolism of yeast mannan by B. thetaiotaomicron presents a 'selfish' model for the catabolism of this difficult to breakdown polysaccharide. Genomic comparison with B. thetaiotaomicron in conjunction with cell culture studies show that a cohort of highly successful members of the microbiota has evolved to consume sterically-restricted yeast glycans, an adaptation that may reflect the incorporation of eukaryotic microorganisms into the human diet.

  • Organizational Affiliation

    Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLYCOSYL HYDROLASE FAMILY 71380Bacteroides xylanisolvens XB1AMutation(s): 0 
Find proteins for D6D1V7 (Bacteroides xylanisolvens XB1A)
Explore D6D1V7 
Go to UniProtKB:  D6D1V7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD6D1V7
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G53402KW
GlyCosmos:  G53402KW
GlyGen:  G53402KW
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.112 
  • R-Value Observed: 0.113 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.469α = 90
b = 108.469β = 90
c = 67.755γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2015-07-15
    Changes: Non-polymer description
  • Version 1.2: 2016-08-10
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary