7LH6

The structure of Bacteroides plebeius L-galactose dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Metabolism of a hybrid algal galactan by members of the human gut microbiome.

Robb, C.S.Hobbs, J.K.Pluvinage, B.Reintjes, G.Klassen, L.Monteith, S.Giljan, G.Amundsen, C.Vickers, C.Hettle, A.G.Hills, R.Xing, X.Montina, T.Zandberg, W.F.Abbott, D.W.Boraston, A.B.

(2022) Nat Chem Biol 18: 501-510

  • DOI: https://doi.org/10.1038/s41589-022-00983-y
  • Primary Citation of Related Structures:  
    7LH6, 7LHA, 7LJJ, 7LNP

  • PubMed Abstract: 

    Native porphyran is a hybrid of porphryan and agarose. As a common element of edible seaweed, this algal galactan is a frequent component of the human diet. Bacterial members of the human gut microbiota have acquired polysaccharide utilization loci (PULs) that enable the metabolism of porphyran or agarose. However, the molecular mechanisms that underlie the deconstruction and use of native porphyran remains incompletely defined. Here, we have studied two human gut bacteria, porphyranolytic Bacteroides plebeius and agarolytic Bacteroides uniformis, that target native porphyran. This reveals an exo-based cycle of porphyran depolymerization that incorporates a keystone sulfatase. In both PULs this cycle also works together with a PUL-encoded agarose depolymerizing machinery to synergistically reduce native porphyran to monosaccharides. This provides a framework for understanding the deconstruction of a hybrid algal galactan, and insight into the competitive and/or syntrophic relationship of gut microbiota members that target rare nutrients.


  • Organizational Affiliation

    Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-galactose dehydrogenaseA [auth B],
B [auth A]
333Phocaeicola plebeius DSM 17135Mutation(s): 0 
Gene Names: BACPLE_01679
UniProt
Find proteins for B5CY82 (Phocaeicola plebeius (strain DSM 17135 / JCM 12973 / M2))
Explore B5CY82 
Go to UniProtKB:  B5CY82
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5CY82
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.754α = 90
b = 84.461β = 90
c = 129.499γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-3000data reduction
HKL-3000data scaling
HKL-3000data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-09
    Type: Initial release
  • Version 1.1: 2022-03-30
    Changes: Database references
  • Version 1.2: 2022-05-11
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description