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Identification
YMDB IDYMDB00283
NameGlycerol
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionGlycerol, also known as glycerin or glycyl alcohol, 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. Glycerol is an extremely weak basic (essentially neutral) compound (based on its pKa). Glycerol exists in all living species, ranging from bacteria to humans. Glycerol is a potentially toxic compound.
Structure
Thumb
Synonyms
  • 1,2,3-Trihydroxypropane
  • Bulbold
  • Cristal
  • Glyceol Opthalgan
  • Glycerin
  • Glycerine
  • Glyceritol
  • Glycerol
  • Glycyl alcohol
  • Glyrol
  • Glysanin
  • IFP
  • Incorporation factor
  • Osmoglyn
  • Propanetriol
  • RG-S
  • Trihydroxypropane
  • Tryhydroxypropane
  • 1,2,3-Propanetriol
  • Glycerolum
  • Glyzerin
  • Gro
  • Oelsuess
  • Concentrated glycerin
  • Glycerin, concentrated
  • e 422
  • Emery 916
  • Mackstat H 66
  • Pricerine 9091
CAS number56-81-5
WeightAverage: 92.0938
Monoisotopic: 92.047344122
InChI KeyPEDCQBHIVMGVHV-UHFFFAOYSA-N
InChIInChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
IUPAC Namepropane-1,2,3-triol
Traditional IUPAC Nameglycerol
Chemical FormulaC3H8O3
SMILES[H]OC([H])([H])C([H])(O[H])C([H])([H])O[H]
Chemical Taxonomy
Description 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.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentSugar alcohols
Alternative Parents
Substituents
  • Sugar alcohol
  • Secondary alcohol
  • Polyol
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateLiquid
Charge0
Melting point20 °C
Experimental Properties
PropertyValueReference
Water Solubility1000 mg/mL at 25 oC [YALKOWSKY,SH & DANNENFELSER,RM (1992)]PhysProp
LogP-1.76 [HANSCH,C ET AL. (1995)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility1170 g/LALOGPS
logP-1.9ALOGPS
logP-1.8ChemAxon
logS1.1ALOGPS
pKa (Strongest Acidic)13.61ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area60.69 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity20.52 m³·mol⁻¹ChemAxon
Polarizability8.93 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • extracellular
  • cytoplasm
Organoleptic Properties
Flavour/OdourSource
OdorlessFDB000756
SMPDB Pathways
Triacylglycerol metabolism TG(10:0/10:0/24:0)PW007646 ThumbThumb?image type=greyscaleThumb?image type=simple
Triacylglycerol metabolism TG(10:0/10:0/24:1(15Z))PW007655 ThumbThumb?image type=greyscaleThumb?image type=simple
Triacylglycerol metabolism TG(10:0/10:0/25:0)PW007677 ThumbThumb?image type=greyscaleThumb?image type=simple
Triacylglycerol metabolism TG(10:0/10:0/25:1(15Z))PW007682 ThumbThumb?image type=greyscaleThumb?image type=simple
Triacylglycerol metabolism TG(10:0/10:0/26:0)PW007700 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Galactose metabolismec00052 Map00052
Glycerolipid metabolismec00561 Map00561
SMPDB Reactions
Dihydroxyacetone + NADPH + hydronNADP + Glycerol
Glycerol + NADPGlyceraldehyde + NADPH + hydron
Glycerol + Adenosine triphosphateADP + Glycerol 3-phosphate
water + Glycerol 3-phosphate Glycerol + phosphate
MG(16:0/0:0/0:0) + waterPalmitic acid + hydron + Glycerol
KEGG Reactions
D-glyceraldehyde + NADPH + hydronNADP + Glycerol
NADP + GlycerolDihydroxyacetone + NADPH + hydron
Adenosine triphosphate + GlycerolGlycerol 3-phosphate + hydron + ADP
Glycerol 3-phosphate + waterGlycerol + phosphate
Concentrations
Intracellular Concentrations
Intracellular ConcentrationSubstrateGrowth ConditionsStrainCitation
2250 ± 1750 µM Synthetic medium with 1% glucose and 0.1% yeast extractaerobicBaker's yeastPMID: 16623706
Conversion Details Here
Extracellular Concentrations
Intracellular ConcentrationSubstrateGrowth ConditionsStrainCitation
50 ± 50 µM Synthetic medium with 1% glucose and 0.1% yeast extractaerobicBaker's yeastPMID: 16623706
Conversion Details Here
Spectra
Spectra
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
  • Schwartz, J. M., Kanehisa, M. (2006). "Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis." BMC Bioinformatics 7:186.16584566
  • Ford, G., Ellis, E. M. (2002). "Characterization of Ypr1p from Saccharomyces cerevisiae as a 2-methylbutyraldehyde reductase." Yeast 19:1087-1096.12210903
  • Costenoble, R., Valadi, H., Gustafsson, L., Niklasson, C., Franzen, C. J. (2000). "Microaerobic glycerol formation in Saccharomyces cerevisiae." Yeast 16:1483-1495.11113971
  • Bleve, G., Zacheo, G., Cappello, M. S., Dellaglio, F., Grieco, F. (2005). "Subcellular localization and functional expression of the glycerol uptake protein 1 (GUP1) of Saccharomyces cerevisiae tagged with green fluorescent protein." Biochem J 390:145-155.15813700
  • Xu, Z., Tsurugi, K. (2006). "A potential mechanism of energy-metabolism oscillation in an aerobic chemostat culture of the yeast Saccharomyces cerevisiae." FEBS J 273:1696-1709.16623706
  • Castrillo, J. I., Zeef, L. A., Hoyle, D. C., Zhang, N., Hayes, A., Gardner, D. C., Cornell, M. J., Petty, J., Hakes, L., Wardleworth, L., Rash, B., Brown, M., Dunn, W. B., Broadhurst, D., O'Donoghue, K., Hester, S. S., Dunkley, T. P., Hart, S. R., Swainston, N., Li, P., Gaskell, S. J., Paton, N. W., Lilley, K. S., Kell, D. B., Oliver, S. G. (2007). "Growth control of the eukaryote cell: a systems biology study in yeast." J Biol 6:4.17439666
Synthesis Reference:Yang, Yifang. Purification of glycerol. Faming Zhuanli Shenqing Gongkai Shuomingshu (2007), 3pp.
External Links:
ResourceLink
CHEBI ID17754
HMDB IDHMDB00131
Pubchem Compound ID753
Kegg IDC00116
ChemSpider ID733
FOODB IDFDB000756
WikipediaGlycerol
BioCyc IDGLYCEROL

Enzymes

General function:
Involved in oxidoreductase activity
Specific function:
Unknown function which seems to be not essential
Gene Name:
GCY1
Uniprot ID:
P14065
Molecular weight:
35078.89844
Reactions
General function:
Involved in catalytic activity
Specific function:
Bifunctional enzyme that catalyzes the enolization of 2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P) into the intermediate 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate (HK-MTPenyl-1-P), which is then dephosphorylated to form the acireductone 1,2-dihydroxy-3-keto-5-methylthiopentene (DHK-MTPene)
Gene Name:
UTR4
Uniprot ID:
P32626
Molecular weight:
25187.19922
Reactions
5-(methylthio)-2,3-dioxopentyl phosphate + H(2)O → 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + phosphate.
2-Phosphoglycolate + H2O → glycolate + phosphate
General function:
Involved in catalytic activity
Specific function:
Glycerol 3-phosphate + H(2)O = glycerol + phosphate
Gene Name:
HOR2
Uniprot ID:
P40106
Molecular weight:
27813.5
Reactions
Glycerol 3-phosphate + H(2)O → glycerol + phosphate.
glycerol 1-phosphate + H2O → glycerol + phosphate
General function:
Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:
ATP + glycerol = ADP + sn-glycerol 3- phosphate
Gene Name:
GUT1
Uniprot ID:
P32190
Molecular weight:
79823.60156
Reactions
ATP + glycerol → ADP + sn-glycerol 3-phosphate.
General function:
Involved in catalytic activity
Specific function:
Glycerol 3-phosphate + H(2)O = glycerol + phosphate
Gene Name:
RHR2
Uniprot ID:
P41277
Molecular weight:
27946.59961
Reactions
Glycerol 3-phosphate + H(2)O → glycerol + phosphate.
glycerol 1-phosphate + H2O → glycerol + phosphate
General function:
Involved in catalytic activity
Specific function:
Catalyzes the irreversible reduction of the cytotoxic compound methylglyoxal (MG) to (R)-lactaldehyde as an alternative to detoxification of MG by glyoxalase I GLO1. MG is synthesized via a bypath of glycolysis from dihydroxyacetone phosphate and is believed to play a role in cell cycle regulation and stress adaptation
Gene Name:
GRE2
Uniprot ID:
Q12068
Molecular weight:
38169.19922
Reactions
Lactaldehyde + NADP(+) → methylglyoxal + NADPH.
3-methylbutanol + NAD(P)+ → 3-methylbutanal + NAD(P)H + H+
General function:
Involved in oxidoreductase activity
Specific function:
Reduces the cytotoxic compound methylglyoxal (MG) to (R)-lactaldehyde similar to GRE2. MG is synthesized via a bypath of glycolysis from dihydroxyacetone phosphate and is believed to play a role in cell cycle regulation and stress adaptation. In pentose-fermenting yeasts, aldose reductase catalyzes the reduction of xylose into xylitol. The purified enzyme catalyzes this reaction, but the inability of S.cerevisiae to grow on xylose as sole carbon source indicates that the physiological function is more likely methylglyoxal reduction
Gene Name:
GRE3
Uniprot ID:
P38715
Molecular weight:
37118.5
Reactions
Alditol + NAD(P)(+) → aldose + NAD(P)H.
(R)-lactaldehyde + NADP(+) → methylglyoxal + NADPH.
General function:
Involved in zinc ion binding
Specific function:
NADP-dependent alcohol dehydrogenase with a broad substrate specificity
Gene Name:
ADH7
Uniprot ID:
P25377
Molecular weight:
39348.19922
Reactions
An alcohol + NADP(+) → an aldehyde + NADPH.
General function:
Involved in zinc ion binding
Specific function:
NADP-dependent alcohol dehydrogenase with a broad substrate specificity
Gene Name:
ADH6
Uniprot ID:
Q04894
Molecular weight:
39617.30078
Reactions
An alcohol + NADP(+) → an aldehyde + NADPH.
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
Gene Name:
CRD1
Uniprot ID:
Q07560
Molecular weight:
32019.30078
Reactions
2 Phosphatidylglycerol → diphosphatidylglycerol + glycerol.
General function:
Involved in oxidoreductase activity
Specific function:
Not Available
Gene Name:
YPR1
Uniprot ID:
Q12458
Molecular weight:
34754.69922
Reactions
General function:
Involved in catalytic activity
Specific function:
Not Available
Gene Name:
Not Available
Uniprot ID:
Q12486
Molecular weight:
24839.80078
Reactions
2-Phosphoglycolate + H2O → glycolate + phosphate
General function:
Involved in catalytic activity
Specific function:
Not Available
Gene Name:
Not Available
Uniprot ID:
Q04223
Molecular weight:
35278.10156
Reactions
2-Phosphoglycolate + H2O → glycolate + phosphate
General function:
triglyceride metabolic process
Specific function:
Converts monoacylglycerides (MAG) to free fatty acids and glycerol. Required for efficient degradation of MAG, short-lived intermediates of glycerolipid metabolism which may also function as lipid signaling molecules. Controls inactivation of the signaling lipid N-palmitoylethanolamine (PEA).
Gene Name:
YJU3
Uniprot ID:
P28321
Molecular weight:
35562.4
Reactions

Transporters

General function:
Involved in transmembrane transporter activity
Specific function:
Not Available
Gene Name:
STL1
Uniprot ID:
P39932
Molecular weight:
63531.19922
General function:
Involved in transporter activity
Specific function:
Channel protein for glycerol. Has a role in both glycerol influx and efflux. Plays a role in osmoregulation:under osmotic stress the channel is apparently closed to allow accumulation of glycerol in the cell under hyperosmotic conditions
Gene Name:
FPS1
Uniprot ID:
P23900
Molecular weight:
73876.89844