P. aeruginosa Metabolome Database: Glycerol (PAMDB000050)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 11:54:54 AM

Metabolite ID

PAMDB000050

Identification

Name:

Glycerol

Description:

Glycerol is an organic compound, also called glycerin or glycerine. It is a colorless, odorless, viscous liquid that is widely used in pharmaceutical formulations. Glycerol has three hydrophilic hydroxyl groups that are responsible for its solubility in water and its hygroscopic nature. Metabolism of glycerol in Pseudomonas aeruginosa, generally requires the presence of external electron acceptors. The respiratory pathways mediating this metabolic process involve a glycerol transporter (encoded by glpF), a glycerol kinase (encoded by glpK), and two respiratory glycerol-3-phosphate dehydrogenases (G3PDHs). Glycerol may also be metabolized fermentatively leading to the production of ethanol.

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

1,2,3-Trihydroxypropane
1,2,3-Trihydroxypropanol
Bulbold
Cristal
E 422
Emery 916
Glyceol Opthalgan
Glycerin
Glycerine
Glyceritol
Glycerol
Glycyl alcohol
Glyrol
Glysanin
IFP
Incorporation factor
Mackstat H 66
Osmoglyn
Pricerine 9091
Propanetriol
RG-S
Trihydroxypropane
Tryhydroxypropane

Chemical Formula:

C₃H₈O₃

Average Molecular Weight:

92.0938

Monoisotopic Molecular Weight:

92.047344122

InChI Key:

PEDCQBHIVMGVHV-UHFFFAOYSA-N

InChI:

InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2

CAS number:

56-81-5

IUPAC Name:

propane-1,2,3-triol

Traditional IUPAC Name:

glycerol

SMILES:

OCC(O)CO

Chemical Taxonomy

Taxonomy Description

This compound belongs to the class of organic compounds known as sugar alcohols. These are hydrogenated forms of carbohydrate in which the carbonyl group (aldehyde or ketone, reducing sugar) has been reduced to a primary or secondary hydroxyl group.

Kingdom

Organic compounds

Super Class

Organooxygen compounds

Class

Carbohydrates and carbohydrate conjugates

Sub Class

Sugar alcohols

Direct Parent

Sugar alcohols

Alternative Parents

Substituents

Sugar alcohol
Secondary alcohol
Polyol
1,2-diol
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

triol (CHEBI:17754 )
alditol (CHEBI:17754 )
Glycerols (C00116 )
a sugar alcohol (GLYCEROL )

Physical Properties

State:

Liquid

Charge:

Melting point:

Experimental Properties:

Property	Value	Source
Water Solubility:	1000.0 mg/mL [YALKOWSKY,SH & DANNENFELSER,RM (1992)]	PhysProp
LogP:	-1.76 [HANSCH,C ET AL. (1995)]	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	1170.0 mg/mL	ALOGPS
logP	-1.9	ALOGPS
logP	-1.8	ChemAxon
logS	1.1	ALOGPS
pKa (Strongest Acidic)	13.61	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	60.69 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	20.52 m³·mol^-1	ChemAxon
Polarizability	8.93 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:

Cytoplasm

Reactions:

D-Glyceraldehyde + Hydrogen ion + NADH <> Glycerol + NAD
Glycerol 3-phosphate + Water > Glycerol + Phosphate
Glycerophosphoglycerol + Water > Glycerol + Glycerol 3-phosphate + Hydrogen ion
Glycerol 2-phosphate + Water > Glycerol + Phosphate
Adenosine triphosphate + Glycerol <> ADP + Glycerol 3-phosphate + Hydrogen ion
Glycerol + NAD <> Dihydroxyacetone + Hydrogen ion + NADH
Adenosine triphosphate + Glycerol <> ADP + Glycerol 3-phosphate
2 Phosphatidylglycerol <> Cardiolipin + Glycerol
an L-1-phosphatidyl-glycerol <> a cardiolipin + Glycerol
glycerol 1-phosphate + Water Glycerol + Phosphate
2 Phosphatidylglycerol > diphosphatidylglycerol + Glycerol

More...

Pathways:

Galactose metabolism pae00052
Glycerolipid metabolism pae00561
Metabolic pathways pae01100
Propanoate metabolism pae00640

Spectra

Spectra:

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (3 TMS)	splash10-0fr2-0910000000-6497c0870b71585c6322	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (3 TMS)	splash10-0ktb-0920000000-93408d69acffad6f48af	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (3 TMS)	splash10-05mk-0940000000-778ba583836705f8fdf4	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)	splash10-00kb-0920000000-2e4b358941c660851f0a	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (3 TMS)	splash10-00dj-6920000000-6828d7b00cb31e84fac1	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-0le9-0940000000-e0b9bada9be26d720326	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS	Not Available
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0a4i-9000000000-d7c139dc01453f61eb99	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0a4l-9000000000-7d7844b4813b038012da	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0udi-9100000000-16029dbe79f139ab904a	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - EI-B (HITACHI M-80) , Positive	splash10-01ox-9000000000-3fe0c184a891364773a8	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0006-9000000000-a638e26fe3c3f48563c2	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004l-9000000000-d3fd9e9abd911eb0f88e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a6r-9000000000-ca218dca3a5d86196d81	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-9000000000-b40367f5ca8d11288fbe	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9000000000-ba29a0647084e32d8704	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0abc-9000000000-4cd85379d414c16f95c0	View in MoNA
MS	Mass Spectrum (Electron Ionization)	splash10-01ox-9000000000-3706109441e6d3017895	View in MoNA
1D NMR	1H NMR Spectrum	Not Available
1D NMR	13C NMR Spectrum	Not Available
1D NMR	1H NMR Spectrum	Not Available
1D NMR	13C NMR Spectrum	Not Available
1D NMR	1H NMR Spectrum	Not Available
2D NMR	[1H,1H] 2D NMR Spectrum	Not Available
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available

References

References:

Berger C, Sakowitz OW, Kiening KL, Schwab S: Neurochemical monitoring of glycerol therapy in patients with ischemic brain edema. Stroke. 2005 Feb;36(2):e4-6. Epub 2004 Dec 23. Pubmed: 15618446
Boulat O, Gradwohl M, Matos V, Guignard JP, Bachmann C: Organic acids in the second morning urine in a healthy Swiss paediatric population. Clin Chem Lab Med. 2003 Dec;41(12):1642-58. Pubmed: 14708889
Bulow J, Gjeraa K, Enevoldsen LH, Simonsen L: Lipid mobilization from human abdominal, subcutaneous adipose tissue is independent of sex during steady-state exercise. Clin Physiol Funct Imaging. 2006 Jul;26(4):205-11. Pubmed: 16836692
Coppack SW, Chinkes DL, Miles JM, Patterson BW, Klein S: A multicompartmental model of in vivo adipose tissue glycerol kinetics and capillary permeability in lean and obese humans. Diabetes. 2005 Jul;54(7):1934-41. Pubmed: 15983192
de Araujo Burgos MG, Bion FM, Campos F: [Lactation and alcohol: clinical and nutritional effects] Arch Latinoam Nutr. 2004 Mar;54(1):25-35. Pubmed: 15332353
De Haene H, Taes Y, Christophe A, Delanghe J: Comparison of triglyceride concentration with lipemic index in disorders of triglyceride and glycerol metabolism. Clin Chem Lab Med. 2006;44(2):220-2. Pubmed: 16475911
Ekberg NR, Wisniewski N, Brismar K, Ungerstedt U: Measurement of glucose and metabolites in subcutaneous adipose tissue during hyperglycemia with microdialysis at various perfusion flow rates. Clin Chim Acta. 2005 Sep;359(1-2):53-64. Pubmed: 15939412
Eriksson A, Lindstedt S, Ransnas L, von Wendt L: Deficiency of glycerol kinase (EC 2.7.1.30). Clin Chem. 1983 Apr;29(4):718-22. Pubmed: 6299616
Fluhr JW, Mao-Qiang M, Brown BE, Wertz PW, Crumrine D, Sundberg JP, Feingold KR, Elias PM: Glycerol regulates stratum corneum hydration in sebaceous gland deficient (asebia) mice. J Invest Dermatol. 2003 May;120(5):728-37. Pubmed: 12713573
Foster KJ, Alberti KG, Hinks L, Lloyd B, Postle A, Smythe P, Turnell DC, Walton R: Blood intermediary metabolite and insulin concentrations after an overnight fast: reference ranges for adults, and interrelations. Clin Chem. 1978 Sep;24(9):1568-72. Pubmed: 688619
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
Konig K, Rickels E, Heissler HE, Zumkeller M, Samii M: Artificial elevation of brain tissue glycerol by administration of a glycerol-containing agent. Case report. J Neurosurg. 2001 Apr;94(4):621-3. Pubmed: 11302662
Olbermann M, Grunert A, Bassler KH: [Biokinetic characterization of human glycerin utilization] Infusionsther Klin Ernahr. 1977 Apr;4(2):68-70. Pubmed: 558160
Pecora P, Suraci C, Antonelli M, De Maria S, Marrocco W: Blood glycerol meaning in obese patients. Boll Soc Ital Biol Sper. 1981 Dec 15;57(23):2389-93. Pubmed: 7337752
Quisth V, Enoksson S, Blaak E, Hagstrom-Toft E, Arner P, Bolinder J: Major differences in noradrenaline action on lipolysis and blood flow rates in skeletal muscle and adipose tissue in vivo. Diabetologia. 2005 May;48(5):946-53. Epub 2005 Mar 19. Pubmed: 15778861
Ross SE, Erickson RL, Gerin I, DeRose PM, Bajnok L, Longo KA, Misek DE, Kuick R, Hanash SM, Atkins KB, Andresen SM, Nebb HI, Madsen L, Kristiansen K, MacDougald OA: Microarray analyses during adipogenesis: understanding the effects of Wnt signaling on adipogenesis and the roles of liver X receptor alpha in adipocyte metabolism. Mol Cell Biol. 2002 Aug;22(16):5989-99. Pubmed: 12138207
Sjarif DR, Hellerud C, van Amstel JK, Kleijer WJ, Sperl W, Lacombe D, Sass JO, Beemer FA, Duran M, Poll-The BT: Glycerol kinase deficiency: residual activity explained by reduced transcription and enzyme conformation. Eur J Hum Genet. 2004 Jun;12(6):424-32. Pubmed: 15026783
Sjostrand M, Gudbjornsdottir S, Holmang A, Strindberg L, Ekberg K, Lonnroth P: Measurements of interstitial muscle glycerol in normal and insulin-resistant subjects. J Clin Endocrinol Metab. 2002 May;87(5):2206-11. Pubmed: 11994365
Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. Pubmed: 19212411
Sweatman BC, Farrant RD, Holmes E, Ghauri FY, Nicholson JK, Lindon JC: 600 MHz 1H-NMR spectroscopy of human cerebrospinal fluid: effects of sample manipulation and assignment of resonances. J Pharm Biomed Anal. 1993 Aug;11(8):651-64. Pubmed: 8257730
Titov VN, Lisitsyn DM, Ameliushkina VA, Lupanov VP, Staroverov II, Osipov SG, Kukharchuk VV: [Double bonds of fatty acids, alcohols glycerol, cholesterol and nonpolar serum lipids. Diagnostic value of hypercholesterolemia] Klin Lab Diagn. 2002 May;(5):3-8. Pubmed: 12085703
van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Yaqoob M, Nabi A: Flow injection chemiluminescent assays for glycerol and triglycerides using a co-immobilized enzyme reactor. Luminescence. 2003 Mar-Apr;18(2):67-71. Pubmed: 12687625

Synthesis Reference:

Yang, Yifang. Purification of glycerol. Faming Zhuanli Shenqing Gongkai Shuomingshu (2007), 3pp.

Material Safety Data Sheet (MSDS)

Download (PDF)

Links

External Links:

Resource	Link
CHEBI ID	17754
HMDB ID	HMDB00131
Pubchem Compound ID	753
Kegg ID	C00116
ChemSpider ID	733
Wikipedia	Glycerol
BioCyc ID	GLYCEROL
EcoCyc ID	GLYCEROL
Ligand Expo	GOL

Enzymes

Protein Details

• Glycerophosphoryl diester phosphodiesterase

General function:: Involved in glycerophosphodiester phosphodiesterase activity
Specific function:: Glycerophosphoryl diester phosphodiesterase hydrolyzes deacylated phospholipids to G3P and the corresponding alcohols
Gene Name:: glpQ
Locus Tag:: PA0347
Molecular weight:: 42 kDa

Reactions

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

Protein Details

• Glycerol kinase

General function:: Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:: Key enzyme in the regulation of glycerol uptake and metabolism
Gene Name:: glpK
Locus Tag:: PA3582
Molecular weight:: 56 kDa

Reactions

ATP + glycerol = ADP + sn-glycerol 3-phosphate.

Protein Details

• Inositol-1-monophosphatase

General function:: Involved in phosphatidylinositol phosphorylation
Specific function:: Myo-inositol phosphate + H(2)O = myo-inositol + phosphate
Gene Name:: suhB
Locus Tag:: PA3818
Molecular weight:: 29.5 kDa

Reactions

Myo-inositol phosphate + H(2)O = myo-inositol + phosphate.

Protein Details

• Class B acid phosphatase

General function:: Involved in acid phosphatase activity
Specific function:: Dephosphorylates several organic phosphomonoesters and catalyzes the transfer of low-energy phosphate groups from phosphomonoesters to hydroxyl groups of various organic compounds. Preferentially acts on aryl phosphoesters. Might function as a broad-spectrum dephosphorylating enzyme able to scavenge both 3'- and 5'-nucleotides and also additional organic phosphomonoesters
Gene Name:: aphA
Locus Tag:: PA1409
Molecular weight:: 38 kDa

Reactions

A phosphate monoester + H(2)O = an alcohol + phosphate.

Protein Details

• S-(hydroxymethyl)glutathione dehydrogenase

General function:: Involved in zinc ion binding
Specific function:: Has high formaldehyde dehydrogenase activity in the presence of glutathione and catalyzes the oxidation of normal alcohols in a reaction that is not GSH-dependent. In addition, hemithiolacetals other than those formed from GSH, including omega-thiol fatty acids, also are substrates
Gene Name:: frmA
Locus Tag:: PA3629
Molecular weight:: 39.2 kDa

Reactions

S-(hydroxymethyl)glutathione + NAD(P)(+) = S-formylglutathione + NAD(P)H.
An alcohol + NAD(+) = an aldehyde or ketone + NADH.

Protein Details

• Cardiolipin synthase

General function:: Involved in phosphotransferase activity, for other substituted phosphate groups
Specific function:: Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol. Affects resistance to the gyrase inhibitor novobiocin
Gene Name:: cls
Locus Tag:: PA5394
Molecular weight:: 54.6 kDa

Reactions

2 Phosphatidylglycerol = diphosphatidylglycerol + glycerol.

Protein Details

• Putative cardiolipin synthase ybhO

General function:: Involved in catalytic activity
Specific function:: Catalyzes, in vitro, the phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol. Can also catalyze phosphatidyl group transfer to water to form phosphatidate. Catalyzes little, if any, cardiolipin synthesis in vivo, even when the expression level is very high
Gene Name:: ybhO
Locus Tag:: PA2155
Molecular weight:: 46.5 kDa

Reactions

2 Phosphatidylglycerol = diphosphatidylglycerol + glycerol.

Transporters

Protein Details

• Glycerol uptake facilitator protein

General function:: Involved in transporter activity
Specific function:: Transporter of glycerol across the cytoplasmic membrane, with limited permeability to water and small uncharged compounds such as polyols
Gene Name:: glpF
Locus Tag:: PA3581
Molecular weight:: 28.9 kDa

Glycerol (PAMDB000050)

Structure for Glycerol (PAMDB000050)

Enzymes

Reactions

Reactions

Reactions

Reactions

Reactions

Reactions

Reactions

Transporters