Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44291.04 
• Atom Count: 3003 
• Residue Count: 380 
• Unique protein chains: 1

4UTF

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

• DOI: 10.2210/pdb4UTF/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides xylanisolvens XB1A
• Expression System: Escherichia coli BL21


• Deposited: 2014-07-21 Released: 2014-12-24 
• Deposition Author(s): Cuskin, F., Lowe, E.C., Temple, M.J., Zhu, Y., Pudlo, N.A., Cameron, E.A., Urs, K., Thompson, A.J., Cartmell, A., Rogowski, A., Tolbert, T., Piens, K., Bracke, D., Vervecken, W., Hakki, Z., Speciale, G., Munoz-Munoz, J.L., 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.

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Experimental Data Snapshot

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

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

• PubMed: 25567280 
• DOI: 10.1038/nature13995
• Primary Citation of Related Structures:  
  4C1S, 4C1R


• 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
GLYCOSYL HYDROLASE FAMILY 71	A	380	Bacteroides xylanisolvens XB1A	Mutation(s): 0
Find proteins for D6D1V7 (Bacteroides xylanisolvens XB1A) Go to UniProtKB:  D6D1V7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
IFM	A	5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE Afegostat, isofagomine, (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL C6 H13 N O3 QPYJXFZUIJOGNX-HSUXUTPPSA-N
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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 = 108.469	α = 90.00
b = 108.469	β = 90.00
c = 67.755	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
REFMAC	refinement
REFMAC	phasing
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-07-21 
• Released Date: 2014-12-24 
• Deposition Author(s): Cuskin, F., Lowe, E.C., Temple, M.J., Zhu, Y., Pudlo, N.A., Cameron, E.A., Urs, K., Thompson, A.J., Cartmell, A., Rogowski, A., Tolbert, T., Piens, K., Bracke, D., Vervecken, W., Hakki, Z., Speciale, G., Munoz-Munoz, J.L., 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.

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