9BJX | pdb_00009bjx

GH5_4 endo-beta(1,3/1,4)-glucanase from Segatella copri


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.201 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9BJX

This is version 1.0 of the entry. See complete history

Literature

The molecular basis of cereal mixed-linkage beta-glucan utilization by the human gut bacterium Segatella copri.

Golisch, B.Cordeiro, R.L.Fraser, A.S.C.Briggs, J.Stewart, W.A.Van Petegem, F.Brumer, H.

(2024) J Biological Chem 300: 107625-107625

  • DOI: https://doi.org/10.1016/j.jbc.2024.107625
  • Primary Citation Related Structures: 
    9BAL, 9BAM, 9BJX, 9BMK

  • PubMed Abstract: 

    Mixed-linkage β(1,3)/β(1,4)-glucan (MLG) is abundant in the human diet through the ingestion of cereal grains and is widely associated with healthful effects on metabolism and cholesterol levels. MLG is also a major source of fermentable glucose for the human gut microbiota (HGM). Bacteria from the family Prevotellaceae are highly represented in the HGM of individuals who eat plant-rich diets, including certain indigenous people and vegetarians in postindustrial societies. Here, we have defined and functionally characterized an exemplar Prevotellaceae MLG polysaccharide utilization locus (MLG-PUL) in the type-strain Segatella copri (syn. Prevotella copri) DSM 18205 through transcriptomic, biochemical, and structural biological approaches. In particular, structure-function analysis of the cell-surface glycan-binding proteins and glycoside hydrolases of the S. copri MLG-PUL revealed the molecular basis for glycan capture and saccharification. Notably, syntenic MLG-PULs from human gut, human oral, and ruminant gut Prevotellaceae are distinguished from their counterparts in Bacteroidaceae by the presence of a β(1,3)-specific endo-glucanase from glycoside hydrolase family 5, subfamily 4 (GH5_4) that initiates MLG backbone cleavage. The definition of a family of homologous MLG-PULs in individual species enabled a survey of nearly 2000 human fecal microbiomes using these genes as molecular markers, which revealed global population-specific distributions of Bacteroidaceae- and Prevotellaceae-mediated MLG utilization. Altogether, the data presented here provide new insight into the molecular basis of β-glucan metabolism in the HGM, as a basis for informing the development of approaches to improve the nutrition and health of humans and other animals.


  • Organizational Affiliation
    • Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada.

Macromolecule Content 

  • Total Structure Weight: 168.32 kDa 
  • Atom Count: 12,883 
  • Modeled Residue Count: 1,468 
  • Deposited Residue Count: 1,472 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cellulase (Glycosyl hydrolase family 5)
A, B, C, D
368Segatella copri DSM 18205Mutation(s): 0 
Gene Names: PREVCOP_05101
UniProt
Find proteins for D1PD14 (Segatella copri DSM 18205)
Explore D1PD14 
Go to UniProtKB:  D1PD14
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD1PD14
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.201 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.008α = 90
b = 51.56β = 101.5
c = 157.057γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata 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: 2024-10-09
    Type: Initial release