Choline (YMDB00227)

Identification

YMDB ID

YMDB00227

Name

Choline

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Choline, also known as bilineurine or choline ion, belongs to the class of organic compounds known as cholines. These are organic compounds containing a N,N,N-trimethylethanolammonium cation. Choline is an extremely weak basic (essentially neutral) compound (based on its pKa). Choline exists in all living species, ranging from bacteria to humans. Within yeast, choline participates in a number of enzymatic reactions. In particular, glycerol 3-phosphate and choline can be biosynthesized from glycerophosphocholine through its interaction with the enzyme glycerophosphodiester phosphodiesterase GDE1. In addition, choline can be converted into phosphorylcholine through the action of the enzyme choline kinase. In yeast, choline is involved in the metabolic pathway called the lysolipid incorporation into er pc(18:1(9z)/18:1(9z)) pathway.

Structure

MOL SDF PDB SMILES InChI

Synonyms

(2-Hydroxyethyl)trimethyl ammonium
(2-Hydroxyethyl)trimethylammonium
(beta-hydroxyethyl)trimethylammonium
2-hydroxy-N,N,N-trimethyl-ethanaminium
2-hydroxy-N,N,N-trimethylethanaminium
Bilineurine
Biocolina
Biocoline
Choline
Choline cation
Choline ion
Cholinum
Hepacholine
Hormocline
Lipotril
N,N,N-trimethylethanol-ammonium
N,N,N-trimethylethanolammonium
Neocolina
Paresan
N-Trimethylethanolamine
Trimethylethanolamine
Choline O-sulfate
Citrate, choline
Fagine
Hydroxide, choline
Vidine
Bursine
Chloride, choline
Choline chloride
Choline citrate
Bitartrate, choline
Choline bitartrate
Choline hydroxide
Choline O sulfate
O-Sulfate, choline

CAS number

62-49-7

Weight

Average: 104.1708
Monoisotopic: 104.107539075

InChI Key

OEYIOHPDSNJKLS-UHFFFAOYSA-N

InChI

InChI=1S/C5H14NO/c1-6(2,3)4-5-7/h7H,4-5H2,1-3H3/q+1

IUPAC Name

(2-hydroxyethyl)trimethylazanium

Traditional IUPAC Name

choline

Chemical Formula

C₅H₁₄NO

SMILES

[H]OC([H])([H])C([H])([H])[N+](C([H])([H])[H])(C([H])([H])[H])C([H])([H])[H]

Chemical Taxonomy

Description

belongs to the class of organic compounds known as cholines. These are organic compounds containing a N,N,N-trimethylethanolammonium cation.

Kingdom

Organic compounds

Super Class

Organic nitrogen compounds

Class

Organonitrogen compounds

Sub Class

Quaternary ammonium salts

Direct Parent

Cholines

Alternative Parents

Substituents

Choline
Tetraalkylammonium salt
1,2-aminoalcohol
Alkanolamine
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organic salt
Primary alcohol
Organooxygen compound
Amine
Alcohol
Organic cation
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

cholines (CHEBI:15354 )
Pesticides (C00114 )
a small molecule (CHOLINE )

Physical Properties

State

Solid

Charge

Melting point

Not Available

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	3.61 g/L	ALOGPS
logP	-3.6	ALOGPS
logP	-4.7	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	13.97	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	20.23 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	42.19 m³·mol⁻¹	ChemAxon
Polarizability	12.57 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

extracellular
cell envelope
cytoplasm

Organoleptic Properties

Not Available

SMPDB Pathways

Choline metabolism	PW002494
Glycerophospholipid metabolism	PW002493
Lysolipid incorporation into ER	PW002532
Lysolipid incorporation into ER PC(10:0/10:0)	PW002780
Lysolipid incorporation into ER PC(14:0/14:0)	PW002783

KEGG Pathways

Glycerophospholipid metabolism	ec00564
Glycine, serine and threonine metabolism	ec00260

SMPDB Reactions

PC(16:0/16:0) + water → Choline + hydron + PA(16:0/16:0)

Glycerophosphocholine + water → hydron + Glycerol 3-phosphate + Choline

Glycerophosphocholine + water → Ethanol + Choline

Choline + Adenosine triphosphate → ADP + hydron + Phosphorylcholine

KEGG Reactions

Adenosine triphosphate + Choline ↔ Phosphorylcholine + hydron + ADP

water + Glycerophosphocholine → Glycerol 3-phosphate + Choline + hydron

phosphatidylcholine + water → LPA(16:0/0:0) + Choline

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Intracellular Concentration	Substrate	Growth Conditions	Strain	Citation
970 ± 0 µM	hops, malted barley	anaerobic	Baker's yeast	Alcoholic beverage, beer, regular, all - U.S. Department of Agriculture, Agricultural Research Service. 2010. USDA National Nutrient Database for Standard Reference, Release 23. Nutrient Data Laboratory Home Page
547 ± 0 µM	grape juice	anaerobic	Baker's yeast	Alcoholic beverage, wine, table, red - U.S. Department of Agriculture, Agricultural Research Service. 2010. USDA National Nutrient Database for Standard Reference, Release 23. Nutrient Data Laboratory Home Page
Conversion Details Here

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-05fr-9100000000-69389426dd865af031f9	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-05g0-9300000000-ca1b0086d4882b00b395	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0a4i-0900000000-ea6f9c1150759c5be6c7	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0a4i-1900000000-cadf16d18f093e9b19d6	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0bt9-9100000000-a2c328b7da5435b8e467	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-0udi-0900000000-6a7b57dbdf4560721722	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) 30V, Positive	splash10-0udi-5900000000-87fdeef5275a74e78348	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-0w29-5900000000-9b79cc5ff3b1ce17deb1	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-03di-9200000000-fe62d5a4fbf492493d60	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-IT , positive	splash10-0udi-3900000000-0b37e63e9c6b14a2e397	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-0udi-0900000000-6a7b57dbdf4560721722	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-0udi-5900000000-87fdeef5275a74e78348	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - , positive	splash10-0pb9-1900000000-391c1b7859a03e776123	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-2900000000-43b0f930ff04f7a48a59	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udr-9400000000-ab7cc75a8e0d3cc49449	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-9000000000-0b94edfd44e38b20b8d3	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-9100000000-a738404b52e2f1f6fec1	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-9000000000-c596e40769889223b3dd	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-9000000000-c6fab16d1790976560b5	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
2D NMR	[1H,1H] 2D NMR Spectrum	Not Available	JSpectraViewer
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	JSpectraViewer

References

References:

UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
McMaster, C. R., Bell, R. M. (1994). "Phosphatidylcholine biosynthesis in Saccharomyces cerevisiae. Regulatory insights from studies employing null and chimeric sn-1,2-diacylglycerol choline- and ethanolaminephosphotransferases." J Biol Chem 269:28010-28016.7961735
Alcoholic beverage, beer, regular, all - U.S. Department of Agriculture, Agricultural Research Service. 2010. USDA National Nutrient Database for Standard Reference, Release 23. Nutrient Data Laboratory Home Page
Alcoholic beverage, wine, table, red - U.S. Department of Agriculture, Agricultural Research Service. 2010. USDA National Nutrient Database for Standard Reference, Release 23. Nutrient Data Laboratory Home Page
Rose, K., Rudge, S. A., Frohman, M. A., Morris, A. J., Engebrecht, J. (1995). "Phospholipase D signaling is essential for meiosis." Proc Natl Acad Sci U S A 92:12151-12155.8618862
Fisher, E., Almaguer, C., Holic, R., Griac, P., Patton-Vogt, J. (2005). "Glycerophosphocholine-dependent growth requires Gde1p (YPL110c) and Git1p in Saccharomyces cerevisiae." J Biol Chem 280:36110-36117.16141200
Kim, K., Kim, K. H., Storey, M. K., Voelker, D. R., Carman, G. M. (1999). "Isolation and characterization of the Saccharomyces cerevisiae EKI1 gene encoding ethanolamine kinase." J Biol Chem 274:14857-14866.10329685

Synthesis Reference:

Hasegawa, Yoichi; Hyoda, Shunji; Sawada, Hirotoshi; Baba, Masakatsu. Preparation of high-purity organic carboxylic acid choline salts and choline. Jpn. Kokai Tokkyo Koho (1999), 9 pp.

External Links:

Resource	Link
CHEBI ID	15354
HMDB ID	HMDB00097
Pubchem Compound ID	305
Kegg ID	C00114
ChemSpider ID	73580
FOODB ID	FDB000710
Wikipedia	Choline
BioCyc ID	CPD-563

Enzymes

Protein Details

1. Choline kinase

General function:: Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:: Responsible for phosphatidylcholine synthesis via the CDP-choline pathway. Also exhibits ethanolamine kinase activity but at 14% efficiency compared with choline
Gene Name:: CKI1
Uniprot ID:: P20485
Molecular weight:: 66316.0

Reactions

ATP + choline → ADP + O-phosphocholine.

Protein Details

2. Glycerophosphodiester phosphodiesterase GDE1

General function:: Involved in protein binding
Specific function:: Glycerophosphocholine glycerophosphodiesterase responsible for the hydrolysis of intracellular glycerophosphocholine into glycerol-phosphate and choline. The choline is used for phosphatidyl-choline synthesis. Required for utilization of glycerophosphocholine as phosphate source
Gene Name:: GDE1
Uniprot ID:: Q02979
Molecular weight:: 138013.0

Reactions

A glycerophosphodiester + H(2)O → an alcohol + sn-glycerol 3-phosphate.

Protein Details

3. Probable glycerophosphodiester phosphodiesterase YPL206C

General function:: Involved in glycerophosphodiester phosphodiesterase activity
Specific function:: Probable glycerophosphocholine glycerophosphodiesterase which may be responsible for the hydrolysis of intracellular glycerophosphocholine into glycerol-phosphate and choline. The choline is used for phosphatidyl-choline synthesis
Gene Name:: Not Available
Uniprot ID:: Q08959
Molecular weight:: 37069.39844

Reactions

A glycerophosphodiester + H(2)O → an alcohol + sn-glycerol 3-phosphate.

Protein Details

4. Phospholipase D1

General function:: Involved in protein binding
Specific function:: Required for meiosis and spore formation. Seems to be involved in the coordinate induction of late meiotic events. PLD activity is induced under sporulation conditions and seems to be necessary to complete the meiotic cycle, but not for vegetative cell growth
Gene Name:: SPO14
Uniprot ID:: P36126
Molecular weight:: 195202.0

Reactions

A phosphatidylcholine + H(2)O → choline + a phosphatidate.

Transporters

Protein Details

1. Choline transport protein

General function:: Involved in transport
Specific function:: Sole choline transporter in yeast
Gene Name:: HNM1
Uniprot ID:: P19807
Molecular weight:: 62055.39844

Structure for #<Compound:0x9ae365e4>

Enzymes

Reactions

Reactions

Reactions

Reactions

Transporters