Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 44.27 kDa 
• Atom Count: 3506 
• Modelled Residue Count: 349 
• Deposited 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

• PDB DOI: 10.2210/pdb4UTF/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides xylanisolvens XB1A
• Expression System: Escherichia coli BL21
• Mutation(s): No 


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

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:  
  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.

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Organizational Affiliation: 

Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCOSYL HYDROLASE FAMILY 71	A	380	Bacteroides xylanisolvens XB1A	Mutation(s): 0  Gene Names: BXY_34140 EC: 3.2.1.130
UniProt
Find proteins for D6D1V7 (Bacteroides xylanisolvens XB1A) Explore D6D1V7  Go to UniProtKB:  D6D1V7

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G53402KW GlyCosmos:  G53402KW GlyGen:  G53402KW

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	C [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
IFM	D [auth A]	5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE C6 H13 N O3 QPYJXFZUIJOGNX-HSUXUTPPSA-N
EDO	E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900111	B	2alpha-alpha-mannobiose	Oligosaccharide / Metabolism		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 108.469	α = 90
b = 108.469	β = 90
c = 67.755	γ = 90

Software Package:

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

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
  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