4Q4C

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP and synthetic 1,5-(PP)2-IP4 (1,5-IP8)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Synthesis of Densely Phosphorylated Bis-1,5-Diphospho-myo-Inositol Tetrakisphosphate and its Enantiomer by Bidirectional P-Anhydride Formation.

Capolicchio, S.Wang, H.Thakor, D.T.Shears, S.B.Jessen, H.J.

(2014) Angew.Chem.Int.Ed.Engl. 53: 9508-9511

  • DOI: 10.1002/anie.201404398
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ubiquitous mammalian signaling molecule bis-diphosphoinositol tetrakisphosphate (1,5-(PP)2 -myo-InsP4 , or InsP8 ) displays the most congested three-dimensional array of phosphate groups found in nature. The high charge density, the accumulation ...

    The ubiquitous mammalian signaling molecule bis-diphosphoinositol tetrakisphosphate (1,5-(PP)2 -myo-InsP4 , or InsP8 ) displays the most congested three-dimensional array of phosphate groups found in nature. The high charge density, the accumulation of unstable P-anhydrides and P-esters, the lack of UV absorbance, and low levels of optical rotation constitute severe obstacles to its synthesis, characterization, and purification. Herein, we describe the first procedure for the synthesis of enantiopure 1,5-(PP)2 -myo-InsP4 and 3,5-(PP)2 -myo-InsP4 utilizing a C2 -symmetric P-amidite for desymmetrization and concomitant phosphitylation followed by a one-pot bidirectional P-anhydride-forming reaction that combines sixteen chemical transformations with high efficiency. The configuration of these materials is unambiguously shown by subsequent X-ray analyses of both enantiomers after being individually soaked into crystals of the kinase domain of human diphosphoinositol pentakisphosphate kinase 2.


    Organizational Affiliation

    Department of Chemistry, University of Zürich (UZH), Winterthurerstrasse 190, 8057 Zürich (Switzerland).




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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
I8P
Query on I8P

Download SDF File 
Download CCD File 
A
(1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)]
1D-myo-inositol 1,5-bisdiphosphate 2,3,4,6-tetrakisphosphate
C6 H20 O30 P8
HHQOOERQSFJGEP-SLWYWOEDSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 89.519α = 90.00
b = 110.224β = 90.00
c = 41.381γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CCP4phasing
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
CCP4model building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-04-14 
  • Released Date: 2014-08-06 
  • Deposition Author(s): Wang, H., Shears, S.B.

Revision History 

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2014-09-10
    Type: Database references