4DA5

Choline Kinase alpha acts through a double-displacement kinetic mechanism involving enzyme isomerisation, as determined through enzyme and inhibitor kinetics and structural biology


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Kinetic and mechanistic characterisation of Choline Kinase-alpha.

Hudson, C.S.Knegtel, R.M.Brown, K.Charlton, P.A.Pollard, J.R.

(2013) Biochim Biophys Acta 1834: 1107-1116

  • DOI: 10.1016/j.bbapap.2013.02.008
  • Primary Citation of Related Structures:  
    4DA5

  • PubMed Abstract: 
  • Choline Kinase is a key component of the Kennedy pathway that converts choline into a number of structural and signalling lipids that are essential for cell growth and survival. One member of the family, Choline Kinase-α (ChoKα) is frequently up-regulate ...

    Choline Kinase is a key component of the Kennedy pathway that converts choline into a number of structural and signalling lipids that are essential for cell growth and survival. One member of the family, Choline Kinase-α (ChoKα) is frequently up-regulated in human cancers, and expression of ChoKα is sufficient to transform cells. Consequently ChoKα has been studied as a potential target for therapeutic agents in cancer research. Despite great interest in the enzyme, mechanistic studies have not been reported. In this study, a combination of initial velocity and product inhibition studies, together with the kinetic and structural characterisation of a novel ChoKα inhibitor is used to support a mechanism of action for human ChoKα. Substrate and inhibition kinetics are consistent with an iso double displacement mechanism, in which the γ-phosphate from ATP is transferred to choline in two distinct steps via a phospho-enzyme intermediate. Co-crystal structures, and existing site-specific mutation studies, support an important role for Asp306, in stabilising the phospho-enzyme intermediate. The kinetics also indicate a distinct kinetic (isomerisation) step associated with product release, which may be attributed to a conformational change in the protein to disrupt an interaction between Asp306 and the phosphocholine product, facilitating product release. This study describes a mechanism for ChoKα that is unusual amongst kinases, and highlights the availability of different enzyme states that can be exploited for drug discovery.


    Organizational Affiliation

    Vertex Pharmaceuticals (Europe) Limited, Oxfordshire, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Choline kinase alpha AB457Homo sapiensMutation(s): 0 
Gene Names: CHKACHKCKI
EC: 2.7.1.32 (PDB Primary Data), 2.7.1.82 (PDB Primary Data)
Find proteins for P35790 (Homo sapiens)
Explore P35790 
Go to UniProtKB:  P35790
NIH Common Fund Data Resources
PHAROS:  P35790
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0H7
Query on 0H7

Download Ideal Coordinates CCD File 
A, B
(3R)-1-azabicyclo[2.2.2]oct-3-yl[bis(5-chlorothiophen-2-yl)]methanol
C16 H17 Cl2 N O S2
ZDHSJVXBNDEQSR-NSHDSACASA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0H7Ki:  360   nM  Binding MOAD
0H7Ki :  360   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.84α = 90
b = 121.69β = 90
c = 131.73γ = 90
Software Package:
Software NamePurpose
DNAdata collection
AMoREphasing
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references