5DGH

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP-PNP and 5-(PCP)-IP5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cellular Cations Control Conformational Switching of Inositol Pyrophosphate Analogues.

Hager, A.Wu, M.Wang, H.Brown, N.W.Shears, S.B.Veiga, N.Fiedler, D.

(2016) Chemistry 22: 12406-12414

  • DOI: 10.1002/chem.201601754
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The inositol pyrophosphate messengers (PP-InsPs) are emerging as an important class of cellular regulators. These molecules have been linked to numerous biological processes, including insulin secretion and cancer cell migration, but how they trigger ...

    The inositol pyrophosphate messengers (PP-InsPs) are emerging as an important class of cellular regulators. These molecules have been linked to numerous biological processes, including insulin secretion and cancer cell migration, but how they trigger such a wide range of cellular responses has remained unanswered in many cases. Here, we show that the PP-InsPs exhibit complex speciation behaviour and propose that a unique conformational switching mechanism could contribute to their multifunctional effects. We synthesised non-hydrolysable bisphosphonate analogues and crystallised the analogues in complex with mammalian PPIP5K2 kinase. Subsequently, the bisphosphonate analogues were used to investigate the protonation sequence, metal-coordination properties, and conformation in solution. Remarkably, the presence of potassium and magnesium ions enabled the analogues to adopt two different conformations near physiological pH. Understanding how the intrinsic chemical properties of the PP-InsPs can contribute to their complex signalling outputs will be essential to elucidate their regulatory functions.


    Organizational Affiliation

    Department of Chemistry, Princeton University, Washington Rd., Princeton, New Jersey, 08544, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2
A
330Homo sapiensMutation(s): 0 
Gene Names: PPIP5K2 (HISPPD1, KIAA0433, VIP2)
EC: 2.7.4.21, 2.7.4.24
Find proteins for O43314 (Homo sapiens)
Go to Gene View: PPIP5K2
Go to UniProtKB:  O43314
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
ANP
Query on ANP

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Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
5A3
Query on 5A3

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Download CCD File 
A
Methylenebisphosphonate inositol pentakisphosphate
{[(R)-hydroxy{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]oxy}phosphoryl]methyl}phosphonic acid
C7 H21 O26 P7
IZNCMXVIYGYGJI-AQWRHFAGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 87.900α = 90.00
b = 110.340β = 90.00
c = 41.253γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-08-27 
  • Released Date: 2016-08-10 
  • Deposition Author(s): Wang, H., Shears, S.B.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health SciencesUnited States--

Revision History 

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-08-24
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations, Refinement description