8T8V

Crystal structure of Terrestrivirus inositol pyrophosphate kinase in complex with ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kinase249Terrestrivirus sp.Mutation(s): 0 
Gene Names: Terrestrivirus9_15
UniProt
Find proteins for A0A3G4ZNY6 (Terrestrivirus sp)
Explore A0A3G4ZNY6 
Go to UniProtKB:  A0A3G4ZNY6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3G4ZNY6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.706α = 90
b = 104.656β = 90
c = 102.502γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing

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 States1ZI AES080046-31

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: 2024-02-07
    Changes: Structure summary
  • Version 1.3: 2024-02-14
    Changes: Database references