Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with Scyllo-3-PP-(1,2,4,5)IP4, Mg, and Fluoride ion

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-06-23 Released: 2023-11-15 
  • Deposition Author(s): Zong, G., Wang, H., Shears, S.B.
  • Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

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Biochemical and structural characterization of an inositol pyrophosphate kinase from a giant virus.

Zong, G.Desfougeres, Y.Portela-Torres, P.Kwon, Y.U.Saiardi, A.Shears, S.B.Wang, H.

(2024) EMBO J 43: 462-480

  • DOI: https://doi.org/10.1038/s44318-023-00005-0
  • Primary Citation of Related Structures:  
    8T8U, 8T8V, 8T8W, 8T8X, 8T8Y, 8T8Z, 8T90, 8T91, 8T92, 8T93, 8T95, 8T96, 8T97, 8T98, 8T99, 8TF9, 8TFA

  • PubMed Abstract: 

    Kinases that synthesize inositol phosphates (IPs) and pyrophosphates (PP-IPs) control numerous biological processes in eukaryotic cells. Herein, we extend this cellular signaling repertoire to viruses. We have biochemically and structurally characterized a minimalist inositol phosphate kinase (i.e., TvIPK) encoded by Terrestrivirus, a nucleocytoplasmic large ("giant") DNA virus (NCLDV). We show that TvIPK can synthesize inositol pyrophosphates from a range of scyllo- and myo-IPs, both in vitro and when expressed in yeast cells. We present multiple crystal structures of enzyme/substrate/nucleotide complexes with individual resolutions from 1.95 to 2.6 Å. We find a heart-shaped ligand binding pocket comprising an array of positively charged and flexible side chains, underlying the observed substrate diversity. A crucial arginine residue in a conserved "G-loop" orients the γ-phosphate of ATP to allow substrate pyrophosphorylation. We highlight additional conserved catalytic and architectural features in TvIPK, and support their importance through site-directed mutagenesis. We propose that NCLDV inositol phosphate kinases may have assisted evolution of inositol pyrophosphate signaling, and we discuss the potential biogeochemical significance of TvIPK in soil niches.

  • Organizational Affiliation

    Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diphosphoinositol polyphosphate phosphohydrolase 1148Homo sapiensMutation(s): 0 
EC: (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
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U6J (Subject of Investigation/LOI)
Query on U6J

Download Ideal Coordinates CCD File 
B [auth A](1r,2R,3S,4r,5R,6S)-4-hydroxy-2,3,5,6-tetrakis(phosphonooxy)cyclohexyl trihydrogen diphosphate
C6 H18 O24 P6
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
MG (Subject of Investigation/LOI)
Query on MG

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C [auth A],
D [auth A],
E [auth A]
F (Subject of Investigation/LOI)
Query on F

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.103α = 90
b = 59.571β = 90
c = 62.43γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1ZIAES080046-31

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Database references
  • Version 1.2: 2024-02-14
    Changes: Database references