5W2I

Crystal structure of the core catalytic domain of human inositol phosphate multikinase soaked with C4-analogue of PtdIns(4,5)P2 and ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation 3D Report Full Report



Literature

Structural features of human inositol phosphate multikinase rationalize its inositol phosphate kinase and phosphoinositide 3-kinase activities.

Wang, H.Shears, S.B.

(2017) J Biol Chem 292: 18192-18202

  • DOI: 10.1074/jbc.M117.801845
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Human inositol phosphate multikinase ( <i>Hs </i>IPMK) critically contributes to intracellular signaling through its inositol-1,4,5-trisphosphate (Ins(1,4,5)P <sub>3 </sub>) 3-kinase and phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P <sub>2 </su ...

    Human inositol phosphate multikinase ( Hs IPMK) critically contributes to intracellular signaling through its inositol-1,4,5-trisphosphate (Ins(1,4,5)P 3 ) 3-kinase and phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P 2 ) 3-kinase activities. This catalytic profile is not conserved; orthologs from Arabidopsis thaliana and Saccharomyces cerevisiae are predominantly Ins(1,4,5)P 3 6-kinases, and the plant enzyme cannot phosphorylate PtdIns(4,5)P 2 Therefore, crystallographic analysis of the yeast and plant enzymes, without bound inositol phosphates, do not structurally rationalize Hs IPMK activities. Here, we present 1.6-Å resolution crystal structures of Hs IPMK in complex with either Ins(1,4,5)P 3 or PtdIns(4,5)P 2 The Ins(1,4,5)P 3 headgroup of PtdIns(4,5)P 2 binds in precisely the same orientation as free Ins(1,4,5)P 3 itself, indicative of evolutionary optimization of 3-kinase activities against both substrates. We report on nucleotide binding between the separate N- and C-lobes of Hs IPMK. The N-lobe exhibits a remarkable degree of conservation with protein kinase A (root mean square deviation = 1.8 Å), indicating common ancestry. We also describe structural features unique to Hs IPMK. First, we observed a constrained, horseshoe-shaped substrate pocket, formed from an α-helix, a 3 10 helix, and a recently evolved tri-proline loop. We further found Hs IPMK activities rely on a preponderance of Gln residues, in contrast to the larger Lys and Arg residues in yeast and plant orthologs. These conclusions are supported by analyzing 14 single-site Hs IPMK mutants, some of which differentially affect 3-kinase and 6-kinase activities. Overall, we structurally rationalize phosphorylation of Ins(1,4,5)P 3 and PtdIns(4,5)P 2 by Hs IPMK.


    Organizational Affiliation

    From the Inositol Signaling Group, Signal Transduction Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inositol polyphosphate multikinase,Inositol polyphosphate multikinase
A
257Homo sapiensMutation(s): 0 
Gene Names: IPMKIMPK
EC: 2.7.1.151 (PDB Primary Data), 2.7.1.140 (UniProt), 2.7.1.153 (UniProt)
Find proteins for Q8NFU5 (Homo sapiens)
Go to UniProtKB:  Q8NFU5
NIH Common Fund Data Resources
PHAROS  Q8NFU5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
I3P
Query on I3P

Download CCD File 
A
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
C6 H15 O15 P3
MMWCIQZXVOZEGG-XJTPDSDZSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.09α = 90
b = 78.09β = 90
c = 86.32γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2017-06-06 
  • Released Date: 2017-09-13 
  • Deposition Author(s): Wang, H., Shears, S.B.

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Database references
  • Version 2.0: 2017-12-20
    Changes: Advisory, Atomic model, Database references, Derived calculations
  • Version 3.0: 2018-01-17
    Changes: Advisory, Atomic model, Database references, Derived calculations