7NWR

Structure of BT1526, a myo-inositol-1-phosphate synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.183 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Characterization of inositol lipid metabolism in gut-associated Bacteroidetes.

Heaver, S.L.Le, H.H.Tang, P.Basle, A.Mirretta Barone, C.Vu, D.L.Waters, J.L.Marles-Wright, J.Johnson, E.L.Campopiano, D.J.Ley, R.E.

(2022) Nat Microbiol 7: 986-1000

  • DOI: https://doi.org/10.1038/s41564-022-01152-6
  • Primary Citation of Related Structures:  
    7NWR

  • PubMed Abstract: 

    Inositol lipids are ubiquitous in eukaryotes and have finely tuned roles in cellular signalling and membrane homoeostasis. In Bacteria, however, inositol lipid production is relatively rare. Recently, the prominent human gut bacterium Bacteroides thetaiotaomicron (BT) was reported to produce inositol lipids and sphingolipids, but the pathways remain ambiguous and their prevalence unclear. Here, using genomic and biochemical approaches, we investigated the gene cluster for inositol lipid synthesis in BT using a previously undescribed strain with inducible control of sphingolipid synthesis. We characterized the biosynthetic pathway from myo-inositol-phosphate (MIP) synthesis to phosphoinositol dihydroceramide, determined the crystal structure of the recombinant BT MIP synthase enzyme and identified the phosphatase responsible for the conversion of bacterially-derived phosphatidylinositol phosphate (PIP-DAG) to phosphatidylinositol (PI-DAG). In vitro, loss of inositol lipid production altered BT capsule expression and antimicrobial peptide resistance. In vivo, loss of inositol lipids decreased bacterial fitness in a gnotobiotic mouse model. We identified a second putative, previously undescribed pathway for bacterial PI-DAG synthesis without a PIP-DAG intermediate, common in Prevotella. Our results indicate that inositol sphingolipid production is widespread in host-associated Bacteroidetes and has implications for symbiosis.


  • Organizational Affiliation

    Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Tübingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inositol-3-phosphate synthaseA [auth B],
B [auth A]
449Bacteroides thetaiotaomicronMutation(s): 0 
Gene Names: BatF92_28780DW011_10900DWY18_07415DXA83_12175GAG59_16320GAN91_05515GAN99_14790GAO00_21425HMPREF2534_03028SAMN02910322_01983
UniProt
Find proteins for Q8A7J8 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A7J8 
Go to UniProtKB:  Q8A7J8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A7J8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.183 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.805α = 90
b = 104.563β = 90
c = 124.318γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
xia2data reduction
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V001620/1
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V00168X/1

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-30
    Type: Initial release
  • Version 1.1: 2022-07-20
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description