4O4E

Crystal Structure of an Inositol hexakisphosphate kinase EhIP6KA in complexed with ATP and Ins(1,3,4,5,6)P5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1038/ncomms5178
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inositol hexakisphosphate kinase
A
248Entamoeba histolytica HM-1:IMSS-AMutation(s): 0 
EC: 2.7.-.-
Find proteins for N9UNA8 (Entamoeba histolytica HM-1:IMSS-A)
Go to UniProtKB:  N9UNA8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
5MY
Query on 5MY

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Download CCD File 
A
MYO-INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE
C6 H17 O21 P5
CTPQAXVNYGZUAJ-KXXVROSKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.999α = 90.00
b = 102.999β = 90.00
c = 110.976γ = 90.00
Software Package:
Software NamePurpose
CCP4model building
REFMACrefinement
HKL-2000data scaling
CCP4phasing
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-12-18 
  • Released Date: 2014-06-18 
  • Deposition Author(s): Wang, H., Shears, S.B.

Revision History 

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2014-07-09
    Type: Database references