6EUH

The GH43, Beta 1,3 Galactosidase, BT3683 with galactodeoxynojirimycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1038/s41564-018-0258-8
  • Structures With Same Primary Citation

  • 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 ...

    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.


    Organizational Affiliation

    Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK. harry.gilbert@ncl.ac.uk.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-glucanase
A, B, C
374Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)Mutation(s): 0 
Gene Names: BT_3683
Find proteins for Q8A1H8 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482))
Go to UniProtKB:  Q8A1H8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGJ
Query on DGJ

Download CCD File 
A, B
(2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol
C6 H13 N O4
LXBIFEVIBLOUGU-DPYQTVNSSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.18α = 114
b = 77.2β = 101.78
c = 78.69γ = 100.78
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited Kingdom322820

Revision History 

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection