2CKP

Crystal structure of Human Choline Kinase alpha-2 in complex with ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.256 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Elucidation of Human Choline Kinase Crystal Structures in Complex with the Products Adp or Phosphocholine.

Malito, E.Sekulic, N.Too, W.C.Konrad, M.Lavie, A.

(2006) J.Mol.Biol. 364: 136

  • DOI: 10.1016/j.jmb.2006.08.084
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Choline kinase, responsible for the phosphorylation of choline to phosphocholine as the first step of the CDP-choline pathway for the biosynthesis of phosphatidylcholine, has been recognized as a new target for anticancer therapy. Crystal structures ...

    Choline kinase, responsible for the phosphorylation of choline to phosphocholine as the first step of the CDP-choline pathway for the biosynthesis of phosphatidylcholine, has been recognized as a new target for anticancer therapy. Crystal structures of human choline kinase in its apo, ADP and phosphocholine-bound complexes, respectively, reveal the molecular details of the substrate binding sites. ATP binds in a cavity where residues from both the N and C-terminal lobes contribute to form a cleft, while the choline-binding site constitutes a deep hydrophobic groove in the C-terminal domain with a rim composed of negatively charged residues. Upon binding of choline, the enzyme undergoes conformational changes independently affecting the N-terminal domain and the ATP-binding loop. From this structural analysis and comparison with other kinases, and from mutagenesis data on the homologous Caenorhabditis elegans choline kinase, a model of the ternary ADP.phosphocholine complex was built that reveals the molecular basis for the phosphoryl transfer activity of this enzyme.


    Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHOLINE KINASE ALPHA
A, B
390Homo sapiensMutation(s): 0 
Gene Names: CHKA (CHK, CKI)
EC: 2.7.1.32
Find proteins for P35790 (Homo sapiens)
Go to Gene View: CHKA
Go to UniProtKB:  P35790
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.256 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.271α = 90.00
b = 127.137β = 90.00
c = 158.742γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-04-20 
  • Released Date: 2006-10-04 
  • Deposition Author(s): Malito, E., Lavie, A.

Revision History 

  • Version 1.0: 2006-10-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance