6PCK

Crystal structure of human diphosphoinositol polyphosphate phosphohydrolase 1 in complex with 1-IP7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history


Literature

Vip1 is a kinase and pyrophosphatase switch that regulates inositol diphosphate signaling.

Dollins, D.E.Bai, W.Fridy, P.C.Otto, J.C.Neubauer, J.L.Gattis, S.G.Mehta, K.P.M.York, J.D.

(2020) Proc Natl Acad Sci U S A 117: 9356-9364

  • DOI: https://doi.org/10.1073/pnas.1908875117
  • Primary Citation of Related Structures:  
    6PCK, 6PCL

  • PubMed Abstract: 

    Inositol diphosphates (PP-IPs), also known as inositol pyrophosphates, are high-energy cellular signaling codes involved in nutrient and regulatory responses. We report that the evolutionarily conserved gene product, Vip1, possesses autonomous kinase and pyrophosphatase domains capable of synthesis and destruction of D-1 PP-IPs. Our studies provide atomic-resolution structures of the PP-IP products and unequivocally define that the Vip1 gene product is a highly selective 1-kinase and 1-pyrophosphatase enzyme whose activities arise through distinct active sites. Kinetic analyses of kinase and pyrophosphatase parameters are consistent with Vip1 evolving to modulate levels of 1-IP 7 and 1,5-IP 8 Individual perturbations in kinase and pyrophosphatase activities in cells result in differential effects on vacuolar morphology and osmotic responses. Analogous to the dual-functional key energy metabolism regulator, phosphofructokinase 2, Vip1 is a kinase and pyrophosphatase switch whose 1-PP-IP products play an important role in a cellular adaptation.


  • Organizational Affiliation

    Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diphosphoinositol polyphosphate phosphohydrolase 1148Homo sapiensMutation(s): 0 
Gene Names: NUDT3DIPPDIPP1
EC: 3.6.1.52 (PDB Primary Data), 3.6.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O95989 (Homo sapiens)
Explore O95989 
Go to UniProtKB:  O95989
PHAROS:  O95989
GTEx:  ENSG00000272325 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95989
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.411α = 90
b = 56.612β = 90
c = 62.556γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-13
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description