6S21

Metabolism of multiple glycosaminoglycans by bacteroides thetaiotaomicron is orchestrated by a versatile core genetic locus (BT33494S-sulf)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Metabolism of multiple glycosaminoglycans by Bacteroides thetaiotaomicron is orchestrated by a versatile core genetic locus.

Ndeh, D.Basle, A.Strahl, H.Yates, E.A.McClurgg, U.L.Henrissat, B.Terrapon, N.Cartmell, A.

(2020) Nat Commun 11: 646-646

  • DOI: https://doi.org/10.1038/s41467-020-14509-4
  • Primary Citation of Related Structures:  
    6S20, 6S21

  • PubMed Abstract: 

    The human gut microbiota (HGM), which is critical to human health, utilises complex glycans as its major carbon source. Glycosaminoglycans represent an important, high priority, nutrient source for the HGM. Pathways for the metabolism of various glycosaminoglycan substrates remain ill-defined. Here we perform a biochemical, genetic and structural dissection of the genetic loci that orchestrates glycosaminoglycan metabolism in the organism Bacteroides thetaiotaomicron. Here, we report: the discovery of two previously unknown surface glycan binding proteins which facilitate glycosaminoglycan import into the periplasm; distinct kinetic and genetic specificities of various periplasmic lyases which dictate glycosaminoglycan metabolic pathways; understanding of endo sulfatase activity questioning the paradigm of how the 'sulfation problem' is handled by the HGM; and 3D crystal structures of the polysaccharide utilisation loci encoded sulfatases. Together with comparative genomic studies, our study fills major gaps in our knowledge of glycosaminoglycan metabolism by the HGM.


  • Organizational Affiliation

    Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endo-4-O-sulfatase
A, B, C
513Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
Gene Names: BT_3349
EC: 3.1.6
UniProt
Find proteins for Q8A2F6 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A2F6 
Go to UniProtKB:  Q8A2F6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A2F6
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid
D, E, F
3N/A
Glycosylation Resources
GlyTouCan:  G72094XQ
GlyCosmos:  G72094XQ
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.193 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.905α = 90
b = 93.911β = 90
c = 304.086γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
BALBESphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited Kingdom322820

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-05
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2024-05-15
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary