4UTF

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.112 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1038/nature13995
  • Primary Citation of Related Structures:  

  • 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 foo ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCOSYL HYDROLASE FAMILY 71
A
380Bacteroides xylanisolvens XB1AMutation(s): 0 
Find proteins for D6D1V7 (Bacteroides xylanisolvens XB1A)
Go to UniProtKB:  D6D1V7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IFM
Query on IFM

Download SDF File 
Download CCD File 
A
5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE
Afegostat, isofagomine, (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL
C6 H13 N O3
QPYJXFZUIJOGNX-HSUXUTPPSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.112 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 108.469α = 90.00
b = 108.469β = 90.00
c = 67.755γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
REFMACphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2015-07-15
    Type: Non-polymer description
  • Version 1.2: 2016-08-10
    Type: Database references