6EON

Galactanase BT0290

• PDB DOI:  https://doi.org/10.2210/pdb6EON/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-10-10 Released: 2017-11-29 
• Deposition Author(s): Basle, A., Munoz, J., Gilbert, H.
• Funding Organization(s): Wellcome Trust, European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.178 
• R-Value Work: 0.156 
• R-Value Observed: 0.157 

Literature

A surface endogalactanase in Bacteroides thetaiotaomicron confers keystone status for arabinogalactan degradation.

Cartmell, A., Munoz-Munoz, J., Briggs, J.A., Ndeh, D.A., Lowe, E.C., Basle, A., Terrapon, N., Stott, K., Heunis, T., Gray, J., Yu, L., Dupree, P., Fernandes, P.Z., Shah, S., Williams, S.J., Labourel, A., Trost, M., Henrissat, B., Gilbert, H.J.

(2018) Nat Microbiol 3: 1314-1326

• PubMed: 30349080 
• DOI: https://doi.org/10.1038/s41564-018-0258-8
• Primary Citation of Related Structures:  
  6EON, 6EUF, 6EUG, 6EUH, 6EUI, 6EUJ


• PubMed Abstract: 
  

Glycans are major nutrients for the human gut microbiota (HGM). Arabinogalactan proteins (AGPs) comprise a heterogenous group of plant glycans in which a β1,3-galactan backbone and β1,6-galactan side chains are conserved. Diversity is provided by the variable nature of the sugars that decorate the galactans. The mechanisms by which nutritionally relevant AGPs are degraded in the HGM are poorly understood. Here we explore how the HGM organism Bacteroides thetaiotaomicron metabolizes AGPs. We propose a sequential degradative model in which exo-acting glycoside hydrolase (GH) family 43 β1,3-galactanases release the side chains. These oligosaccharide side chains are depolymerized by the synergistic action of exo-acting enzymes in which catalytic interactions are dependent on whether degradation is initiated by a lyase or GH. We identified two GHs that establish two previously undiscovered GH families. The crystal structures of the exo-β1,3-galactanases identified a key specificity determinant and departure from the canonical catalytic apparatus of GH43 enzymes. Growth studies of Bacteroidetes spp. on complex AGP revealed 3 keystone organisms that facilitated utilization of the glycan by 17 recipient bacteria, which included B. thetaiotaomicron. A surface endo-β1,3-galactanase, when engineered into B. thetaiotaomicron, enabled the bacterium to utilize complex AGPs and act as a keystone organism.

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Organizational Affiliation: 

Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 89.01 kDa 
• Atom Count: 6,791 
• Modelled Residue Count: 754 
• Deposited Residue Count: 779 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A	779	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0  Gene Names: BT_0290
UniProt
Find proteins for Q8AB22 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8AB22  Go to UniProtKB:  Q8AB22

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLA	B [auth A]	alpha-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-PHYPRBDBSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.178 
• R-Value Work: 0.156 
• R-Value Observed: 0.157 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.038	α = 90
b = 101.162	β = 90
c = 143.214	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-11-29 
Deposition Author(s): Basle, A., Munoz, J., Gilbert, H.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	WT097907AIA
European Research Council		322820

Revision History  

• Version 1.0: 2017-11-29
  Type: Initial release
  
• Version 1.1: 2019-06-26
  Changes: Data collection, Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary