1NW1 | pdb_00001nw1

Crystal Structure of Choline Kinase

• PDB DOI: https://doi.org/10.2210/pdb1NW1/pdb

• Classification: TRANSFERASE
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-02-05 Released: 2003-06-10 
• Deposition Author(s): Peisach, D., Gee, P., Kent, C., Xu, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.231 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

The Crystal Structure of Choline Kinase Reveals a Eukaryotic Protein Kinase Fold

Peisach, D., Gee, P., Kent, C., Xu, Z.

(2003) Structure 11: 703-713

• PubMed: 12791258 
• DOI: https://doi.org/10.1016/s0969-2126(03)00094-7
• Primary Citation Related Structures: 
  1NW1


• PubMed Abstract: 
  

  Choline kinase catalyzes the ATP-dependent phosphorylation of choline, the first committed step in the CDP-choline pathway for the biosynthesis of phosphatidylcholine. The 2.0 A crystal structure of a choline kinase from C. elegans (CKA-2) reveals that the enzyme is a homodimeric protein with each monomer organized into a two-domain fold. The structure is remarkably similar to those of protein kinases and aminoglycoside phosphotransferases, despite no significant similarity in amino acid sequence. Comparisons to the structures of other kinases suggest that ATP binds to CKA-2 in a pocket formed by highly conserved and catalytically important residues. In addition, a choline binding site is proposed to be near the ATP binding pocket and formed by several structurally flexible loops.

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Organizational Affiliation: 
• Department of Biological Chemistry, University of Michigan Medical School, 1301 East Catherine Road, Ann Arbor, MI 48109, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 98.68 kDa 
• Atom Count: 6,153 
• Modeled Residue Count: 722 
• Deposited Residue Count: 858 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Choline kinase (49.2 kD)	A, B	429	Caenorhabditis elegans	Mutation(s): 0  EC: 2.7.1.32 (PDB Primary Data), 2.7.1.82 (UniProt)
UniProt
Find proteins for Q22942 (Caenorhabditis elegans) Explore Q22942  Go to UniProtKB:  Q22942

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.231 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.372	α = 90
b = 102.141	β = 90.66
c = 85.369	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-10 
Deposition Author(s): Peisach, D., Gee, P., Kent, C., Xu, Z.

Revision History  

• Version 1.0: 2003-06-10
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-04-30
  Changes: Data collection
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations