Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 117.75 kDa 
• Atom Count: 9,557 
• Modelled Residue Count: 1,008 
• Deposited Residue Count: 1,032 
• Unique protein chains: 1

 5JOW

Bacteroides ovatus Xyloglucan PUL GH43A

• PDB DOI:  https://doi.org/10.2210/pdb5JOW/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides ovatus ATCC 8483
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-05-03 Released: 2016-08-10 
• Deposition Author(s): Thompson, A.J., Hemsworth, G.R., Stepper, J., Sobala, L.F., Coyle, T., Larsbrink, J., Spadiut, O., Stubbs, K.A., Brumer, H., Davies, G.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council, European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.167 
• R-Value Work: 0.125 
• R-Value Observed: 0.127 

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

• PubMed: 27466444 
• DOI: https://doi.org/10.1098/rsob.160142
• Primary Citation of Related Structures:  
  5JOU, 5JOV, 5JOW, 5JOX, 5JOY, 5JOZ, 5JP0


• 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. 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.

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Organizational Affiliation: 

Department of Chemistry, York Structural Biology Laboratory, The University of York, Heslington, York YO10 5DD, UK [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-reducing end alpha-L-arabinofuranosidase BoGH43A	A, B	516	Bacteroides ovatus ATCC 8483	Mutation(s): 0  Gene Names: BACOVA_02654 EC: 3.2.1.55
UniProt
Find proteins for A7LXT8 (Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / BCRC 10623 / CCUG 4943 / NCTC 11153)) Explore A7LXT8  Go to UniProtKB:  A7LXT8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	C [auth A], N [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO	AA [auth B], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.167 
• R-Value Work: 0.125 
• R-Value Observed: 0.127 
• Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.432	α = 90
b = 91.172	β = 90
c = 156.856	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-08-10 
Deposition Author(s): Thompson, A.J., Hemsworth, G.R., Stepper, J., Sobala, L.F., Coyle, T., Larsbrink, J., Spadiut, O., Stubbs, K.A., Brumer, H., Davies, G.J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/K00591X/1
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/I014802/1
European Research Council	United Kingdom	322942

Revision History  

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