4FDT

Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Bacterial Homolog of a Eukaryotic Inositol Phosphate Signaling Enzyme Mediates Cross-kingdom Dialog in the Mammalian Gut.

Stentz, R.Osborne, S.Horn, N.Li, A.W.Hautefort, I.Bongaerts, R.Rouyer, M.Bailey, P.Shears, S.B.Hemmings, A.M.Brearley, C.A.Carding, S.R.

(2014) Cell Rep 6: 646-656

  • DOI: https://doi.org/10.1016/j.celrep.2014.01.021
  • Primary Citation of Related Structures:  
    4FDT, 4FDU

  • PubMed Abstract: 

    Dietary InsP6 can modulate eukaryotic cell proliferation and has complex nutritive consequences, but its metabolism in the mammalian gastrointestinal tract is poorly understood. Therefore, we performed phylogenetic analyses of the gastrointestinal microbiome in order to search for candidate InsP6 phosphatases. We determined that prominent gut bacteria express homologs of the mammalian InsP6 phosphatase (MINPP) and characterized the enzyme from Bacteroides thetaiotaomicron (BtMinpp). We show that BtMinpp has exceptionally high catalytic activity, which we rationalize on the basis of mutagenesis studies and by determining its crystal structure at 1.9 Å resolution. We demonstrate that BtMinpp is packaged inside outer membrane vesicles (OMVs) protecting the enzyme from degradation by gastrointestinal proteases. Moreover, we uncover an example of cross-kingdom cell-to-cell signaling, showing that the BtMinpp-OMVs interact with intestinal epithelial cells to promote intracellular Ca(2+) signaling. Our characterization of BtMinpp offers several directions for understanding how the microbiome serves human gastrointestinal physiology.


  • Organizational Affiliation

    Gut Health and Food Safety Programme, Institute of Food Research, Norwich NR4 7UA, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative multiple inositol polyphosphate histidine phosphatase 1
A, B
426Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
Gene Names: BT_4744
UniProt
Find proteins for Q89YI8 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q89YI8 
Go to UniProtKB:  Q89YI8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ89YI8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.72α = 90
b = 120.64β = 107.89
c = 76.07γ = 90
Software Package:
Software NamePurpose
DNAdata collection
SOLVEphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2014-03-12
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations