4C1S | pdb_00004c1s

Glycoside hydrolase family 76 (mannosidase) Bt3792 from Bacteroides thetaiotaomicron VPI-5482


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.253 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4C1S

This is version 1.4 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.J.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.Boraston, A.B.Atherly, T.Ziemer, C.J.Williams, S.J.Davies, G.J.Abbott, D.W.Martens, E.C.Gilbert, H.J.

(2015) Nature 517: 165

  • DOI: https://doi.org/10.1038/nature13995
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 87.85 kDa 
  • Atom Count: 6,437 
  • Modeled Residue Count: 750 
  • Deposited Residue Count: 750 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GLYCOSIDE HYDROLASE FAMILY 76 MANNOSIDASE
A, B
375Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
Gene Names: BT3792
EC: 3.2.1.101
UniProt
Find proteins for Q8A174 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A174 
Go to UniProtKB:  Q8A174
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A174
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
L [auth A],
Q [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.253 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.1α = 90
b = 44.42β = 101.43
c = 103.05γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
AutoProcessdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-13
    Type: Initial release
  • Version 1.1: 2014-11-26
    Changes: Database references
  • Version 1.2: 2014-12-24
    Changes: Database references
  • Version 1.3: 2015-03-04
    Changes: Database references
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description