5IJJ | pdb_00005ijj

Structure of the SPX domain of Chaetomium thermophilum Glycerophosphodiester Phosphodiesterase 1 in complex with inositol hexakisphosphate (InsP6)

• PDB DOI: https://doi.org/10.2210/pdb5IJJ/pdb

• Classification: inositol polyphosphate binding protein
• Organism(s): Thermochaetoides thermophila
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-02 Released: 2016-04-27 
• Deposition Author(s): Wild, R., Hothorn, M.
• Funding Organization(s): European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

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

• PubMed: 27080106 
• DOI: https://doi.org/10.1126/science.aad9858
• Primary Citation Related Structures: 
  5IIG, 5IIQ, 5IIT, 5IJH, 5IJJ, 5IJP


• 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. 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.

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Organizational Affiliation: 
• Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.
Department of Biochemistry, University of Lausanne, Lausanne, Switzerland.
Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland.
Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany.
Department of Chemistry and Pharmacy, University of Zürich, Zürich, Switzerland.
Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK.
Department of Chemistry and Pharmacy, University of Zürich, Zürich, Switzerland. Institute of Organic Chemistry, Albert-Ludwigs-University Freiburg, Freiburg, Germany.
Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland. [e-mail] [e-mail] [e-mail].
Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland. [e-mail] [e-mail] [e-mail].
Department of Biochemistry, University of Lausanne, Lausanne, Switzerland. [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 46.86 kDa 
• Atom Count: 2,893 
• Modeled Residue Count: 332 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPX domain	A, B	192	Thermochaetoides thermophila	Mutation(s): 0  Gene Names: CTHT_0005190 EC: 3.1.4.46
UniProt
Find proteins for G0RY29 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0RY29  Go to UniProtKB:  G0RY29

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP	C [auth A], G [auth B], H [auth B]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N
EDO	D [auth A], E [auth A], I [auth B], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.363	α = 90
b = 53.366	β = 113.42
c = 94.314	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
European Research Council	Switzerland	310856

Revision History  

• Version 1.0: 2016-04-27
  Type: Initial release
  
• Version 1.1: 2016-06-01
  Changes: Database references
• Version 2.0: 2020-10-07
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description