Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 105.56 kDa 
• Atom Count: 5951 
• Residue Count: 682 
• Unique protein chains: 1

4DA5

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

• DOI: 10.2210/pdb4DA5/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-01-12 Released: 2013-04-17 
• Deposition Author(s): Brown, K., Hudson, C., Charlton, P., Pollard, J.

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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 

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

• PubMed: 23416529 
• 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-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.

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Organizational Affiliation: 

Vertex Pharmaceuticals (Europe) Limited, Oxfordshire, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Choline kinase alpha	A, B	457	Homo sapiens	Mutation(s): 0  Gene Names: CHKA, CHK, CKI 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 GTEx:  ENSG00000110721

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0H7	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
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
0H7	Ki:  360   nM  Binding MOAD
0H7	Ki :  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 = 55.84	α = 90
b = 121.69	β = 90
c = 131.73	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
AMoRE	phasing
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-12 
• Released Date: 2013-04-17 
Deposition Author(s): Brown, K., Hudson, C., Charlton, P., Pollard, J.

Revision History 

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