5JOX

Bacteroides ovatus Xyloglucan PUL GH43A in complex with AraDNJ


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

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 Biol 6

  • DOI: 10.1098/rsob.160142
  • Primary Citation of Related Structures:  
    5JOU, 5JOW, 5JOV, 5JOY, 5JOX, 5JP0, 5JOZ

  • 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 otherwise recalcitrant to assimilation ...

    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

    Department of Chemistry, York Structural Biology Laboratory, The University of York, Heslington, York YO10 5DD, UK gideon.davies@york.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-reducing end alpha-L-arabinofuranosidase BoGH43A AB516Bacteroides ovatusMutation(s): 0 
Gene Names: BACOVA_02654
EC: 3.2.1.55
Find proteins for A7LXT8 (Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153))
Explore A7LXT8 
Go to UniProtKB:  A7LXT8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDG
Query on EDG

Download Ideal Coordinates CCD File 
A, B
1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL
C5 H11 N O3
OQEBIHBLFRADNM-YUPRTTJUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EDGKd:  35000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.778α = 90
b = 91.626β = 90
c = 154.44γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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  (Full details and data files)

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