7KV2

Surface glycan-binding protein A from Bacteroides thetaiotaomicron


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Distinct protein architectures mediate species-specific beta-glucan binding and metabolism in the human gut microbiota.

Tamura, K.Dejean, G.Van Petegem, F.Brumer, H.

(2021) J Biol Chem 296: 100415-100415

  • DOI: https://doi.org/10.1016/j.jbc.2021.100415
  • Primary Citation of Related Structures:  
    7KV1, 7KV2, 7KV3, 7KV4, 7KV5, 7KV6, 7KV7, 7KWB, 7KWC

  • PubMed Abstract: 

    Complex glycans that evade our digestive system are major nutrients that feed the human gut microbiota (HGM). The prevalence of Bacteroidetes in the HGM of populations worldwide is engendered by the evolution of polysaccharide utilization loci (PULs), which encode concerted protein systems to utilize the myriad complex glycans in our diets. Despite their crucial roles in glycan recognition and transport, cell-surface glycan-binding proteins (SGBPs) remained understudied cogs in the PUL machinery. Here, we report the structural and biochemical characterization of a suite of SGBP-A and SGBP-B structures from three syntenic β(1,3)-glucan utilization loci (1,3GULs) from Bacteroides thetaiotaomicron (Bt), Bacteroides uniformis (Bu), and B. fluxus (Bf), which have varying specificities for distinct β-glucans. Ligand complexes provide definitive insight into β(1,3)-glucan selectivity in the HGM, including structural features enabling dual β(1,3)-glucan/mixed-linkage β(1,3)/β(1,4)-glucan-binding capability in some orthologs. The tertiary structural conservation of SusD-like SGBPs-A is juxtaposed with the diverse architectures and binding modes of the SGBPs-B. Specifically, the structures of the trimodular BtSGBP-B and BuSGBP-B revealed a tandem repeat of carbohydrate-binding module-like domains connected by long linkers. In contrast, BfSGBP-B comprises a bimodular architecture with a distinct β-barrel domain at the C terminus that bears a shallow binding canyon. The molecular insights obtained here contribute to our fundamental understanding of HGM function, which in turn may inform tailored microbial intervention therapies.


  • Organizational Affiliation

    Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, The Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RagB/SusD family nutrient uptake outer membrane proteinA [auth AAA]515Bacteroides thetaiotaomicronMutation(s): 0 
Gene Names: DW011_12550DW780_14665DWY18_18425GAN67_20195GAN98_19115
UniProt
Find proteins for A0A173VPY3 (Bacteroides thetaiotaomicron)
Explore A0A173VPY3 
Go to UniProtKB:  A0A173VPY3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A173VPY3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.83α = 90
b = 71.685β = 105.099
c = 75.068γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release
  • Version 1.1: 2021-03-03
    Changes: Database references
  • Version 1.2: 2021-07-21
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references