5IIQ

Structure of the SPX-TTM domain fragment of the yeast inorganic polyphophate polymerase Vtc4 (form B).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Control of eukaryotic phosphate homeostasis by inositol polyphosphate sensor domains.

Wild, R.Gerasimaite, R.Jung, J.Y.Truffault, V.Pavlovic, I.Schmidt, A.Saiardi, A.Jessen, H.J.Poirier, Y.Hothorn, M.Mayer, A.

(2016) Science 352: 986-990

  • DOI: 10.1126/science.aad9858
  • Primary Citation of Related Structures:  
    5IIQ, 5IIT, 5IIG, 5IJP, 5IJH, 5IJJ

  • PubMed Abstract: 
  • Phosphorus is a macronutrient taken up by cells as inorganic phosphate (P(i)). How cells sense cellular P(i) levels is poorly characterized. Here, we report that SPX domains--which are found in eukaryotic phosphate transporters, signaling proteins, and inorganic polyphosphate polymerases--provide a basic binding surface for inositol polyphosphate signaling molecules (InsPs), the concentrations of which change in response to P(i) availability ...

    Phosphorus is a macronutrient taken up by cells as inorganic phosphate (P(i)). How cells sense cellular P(i) levels is poorly characterized. Here, we report that SPX domains--which are found in eukaryotic phosphate transporters, signaling proteins, and inorganic polyphosphate polymerases--provide a basic binding surface for inositol polyphosphate signaling molecules (InsPs), the concentrations of which change in response to P(i) availability. Substitutions of critical binding surface residues impair InsP binding in vitro, inorganic polyphosphate synthesis in yeast, and P(i) transport in Arabidopsis In plants, InsPs trigger the association of SPX proteins with transcription factors to regulate P(i) starvation responses. We propose that InsPs communicate cytosolic P(i) levels to SPX domains and enable them to interact with a multitude of proteins to regulate P(i) uptake, transport, and storage in fungi, plants, and animals.


    Organizational Affiliation

    Department of Biochemistry, University of Lausanne, Lausanne, Switzerland. yves.poirier@unil.ch michael.hothorn@unige.ch andreas.mayer@unil.ch.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vacuolar transporter chaperone 4A485Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: VTC4PHM3YJL012CJ1345
UniProt
Find proteins for P47075 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47075 
Go to UniProtKB:  P47075
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

Download Ideal Coordinates CCD File 
E [auth A]PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.041α = 90
b = 92.041β = 90
c = 301.732γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-03-01 
  • Released Date: 2016-04-27 
  • Deposition Author(s): Wild, R., Hothorn, M.

Funding OrganizationLocationGrant Number
European Reseacrh CouncilSwitzerland310856

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-06-01
    Changes: Database references