5JOV

Bacteroides ovatus Xyloglucan PUL GH31 with bound 5FIdoF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.107 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural dissection of a complex Bacteroides ovatus gene locus conferring xyloglucan metabolism in the human gut.

Hemsworth, G.R.Thompson, A.J.Stepper, J.Sobala, F.Coyle, T.Larsbrink, J.Spadiut, O.Goddard-Borger, E.D.Stubbs, K.A.Brumer, H.Davies, G.J.

(2016) Open Biology 6: --

  • DOI: 10.1098/rsob.160142
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The human gastrointestinal tract harbours myriad bacterial species, collectively termed the microbiota, that strongly influence human health. Symbiotic members of our microbiota play a pivotal role in the digestion of complex carbohydrates that are o ...

    The human gastrointestinal tract harbours myriad bacterial species, collectively termed the microbiota, that strongly influence human health. Symbiotic members of our microbiota play a pivotal role in the digestion of complex carbohydrates that are otherwise recalcitrant to assimilation. Indeed, the intrinsic human polysaccharide-degrading enzyme repertoire is limited to various starch-based substrates; more complex polysaccharides demand microbial degradation. Select Bacteroidetes are responsible for the degradation of the ubiquitous vegetable xyloglucans (XyGs), through the concerted action of cohorts of enzymes and glycan-binding proteins encoded by specific xyloglucan utilization loci (XyGULs). Extending recent (meta)genomic, transcriptomic and biochemical analyses, significant questions remain regarding the structural biology of the molecular machinery required for XyG saccharification. Here, we reveal the three-dimensional structures of an α-xylosidase, a β-glucosidase, and two α-l-arabinofuranosidases from the Bacteroides ovatus XyGUL. Aided by bespoke ligand synthesis, our analyses highlight key adaptations in these enzymes that confer individual specificity for xyloglucan side chains and dictate concerted, stepwise disassembly of xyloglucan oligosaccharides. In harness with our recent structural characterization of the vanguard endo-xyloglucanse and cell-surface glycan-binding proteins, the present analysis provides a near-complete structural view of xyloglucan recognition and catalysis by XyGUL proteins.


    Organizational Affiliation

    Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden Michael Smith Laboratories and Department of Chemistry, University of British Columbia, 2185 East Mall, Vancouver, British Columbia, Canada V6T 1Z4 brumer@msl.ubc.ca.,Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden Michael Smith Laboratories and Department of Chemistry, University of British Columbia, 2185 East Mall, Vancouver, British Columbia, Canada V6T 1Z4.,Department of Chemistry, York Structural Biology Laboratory, The University of York, Heslington, York YO10 5DD, UK gideon.davies@york.ac.uk.,School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia 6009, Australia.,Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden Wallenberg Wood Science Center, Royal Institute of Technology (KTH), Teknikringen 56-58, 100 44 Stockholm, Sweden.,The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville Victoria 3052, Australia.,Department of Chemistry, York Structural Biology Laboratory, The University of York, Heslington, York YO10 5DD, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-xylosidase BoGH31A
A
955Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153)Mutation(s): 0 
EC: 3.2.1.177
Find proteins for A7LXT0 (Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153))
Go to UniProtKB:  A7LXT0
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
B9D
Query on B9D

Download SDF File 
Download CCD File 
A
(2R,3R,4R,5S,6R)-6-fluoranyl-6-(hydroxymethyl)oxane-2,3,4,5-tetrol
C6 H11 F O6
YQZCKDSOGGIGPL-DVKNGEFBSA-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
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.107 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.906α = 90.00
b = 108.448β = 90.00
c = 144.853γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K00591X/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/I014802/1
European Research CouncilUnited Kingdom322942

Revision History 

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Author supporting evidence