Crystal Structure of an Inositol hexakisphosphate kinase EhIP6KA in complexed with ATP and InsP6

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

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IP6K structure and the molecular determinants of catalytic specificity in an inositol phosphate kinase family.

Wang, H.DeRose, E.F.London, R.E.Shears, S.B.

(2014) Nat Commun 5: 4178-4178

  • DOI: https://doi.org/10.1038/ncomms5178
  • Primary Citation of Related Structures:  
    4O4B, 4O4C, 4O4D, 4O4E, 4O4F

  • PubMed Abstract: 

    Inositol trisphosphate kinases (IP3Ks) and inositol hexakisphosphate kinases (IP6Ks) each regulate specialized signalling activities by phosphorylating either InsP3 or InsP6 respectively. The molecular basis for these different kinase activities can be illuminated by a structural description of IP6K. Here we describe the crystal structure of an Entamoeba histolytica hybrid IP6K/IP3K, an enzymatic parallel to a 'living fossil'. Through molecular modelling and mutagenesis, we extrapolated our findings to human IP6K2, which retains vestigial IP3K activity. Two structural elements, an α-helical pair and a rare, two-turn 310 helix, together forge a substrate-binding pocket with an open clamshell geometry. InsP6 forms substantial contacts with both structural elements. Relative to InsP6, enzyme-bound InsP3 rotates 55° closer to the α-helices, which provide most of the protein's interactions with InsP3. These data reveal the molecular determinants of IP6K activity, and suggest an unusual evolutionary trajectory for a primordial kinase that could have favored efficient bifunctionality, before propagation of separate IP3Ks and IP6Ks.

  • Organizational Affiliation

    Inositol Signaling Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, NC 27709, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inositol hexakisphosphate kinase248Entamoeba histolytica HM-1:IMSS-AMutation(s): 0 
Gene Names: EHI7A_103520
Find proteins for N9UNA8 (Entamoeba histolytica HM-1:IMSS-A)
Explore N9UNA8 
Go to UniProtKB:  N9UNA8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupN9UNA8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.229α = 90
b = 102.229β = 90
c = 109.493γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CCP4model building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2014-07-09
    Changes: Database references
  • Version 1.2: 2020-10-14
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Refinement description