6EUG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.136 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: 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.


  • Organizational Affiliation

    Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-glucanase374Bacteroides thetaiotaomicronMutation(s): 0 
Gene Names: bglA_4BJP75_03275Btheta7330_04612ERS852430_04551HMPREF2534_02351
EC: 3.2.1.73
UniProt
Find proteins for Q8A1H8 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A1H8 
Go to UniProtKB:  Q8A1H8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A1H8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GIM
Query on GIM

Download Ideal Coordinates CCD File 
B [auth A]GLUCOIMIDAZOLE
C8 H13 N2 O4
RZRDQZQPTISYKY-MVIOUDGNSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.136 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.402α = 90
b = 135.402β = 90
c = 51.695γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited Kingdom322820

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references