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Glycogen (YMDB00881)

Identification
YMDB IDYMDB00881
NameGlycogen
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionGlycogen, also known as animal starch or liver starch, belongs to the class of organic compounds known as oligosaccharides. These are carbohydrates made up of 3 to 10 monosaccharide units linked to each other through glycosidic bonds. Glycogen is an extremely weak basic (essentially neutral) compound (based on its pKa). Glycogen exists in all living species, ranging from bacteria to humans. Within yeast, glycogen participates in a number of enzymatic reactions. In particular, glycogen can be biosynthesized from amylose; which is mediated by the enzyme 1,4-alpha-glucan-branching enzyme. In addition, glycogen can be biosynthesized from α-D-glucose; which is catalyzed by the enzyme maltase-glucoamylase, intestinal. In yeast, glycogen is involved in the metabolic pathway called the starch and sucrose metabolism pathway. Glycogen is a potentially toxic compound.
Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
  • Glycogen
  • Lyoglycogen
  • Phytoglycogen
  • Animal starch
  • Liver starch
CAS number9005-79-2
WeightAverage: 666.5777
Monoisotopic: 666.221858406
InChI KeyBYSGBSNPRWKUQH-UJDJLXLFSA-N
InChIInChI=1S/C24H42O21/c25-1-5-9(28)11(30)16(35)22(41-5)39-4-8-20(45-23-17(36)12(31)10(29)6(2-26)42-23)14(33)18(37)24(43-8)44-19-7(3-27)40-21(38)15(34)13(19)32/h5-38H,1-4H2/t5-,6-,7-,8-,9-,10-,11+,12+,13-,14-,15-,16-,17-,18-,19-,20-,21+,22+,23-,24-/m1/s1
IUPAC Name(2R,3R,4S,5S,6R)-2-{[(2R,3S,4R,5R,6R)-4,5-dihydroxy-6-{[(2R,3S,4R,5R,6S)-4,5,6-trihydroxy-2-(hydroxymethyl)oxan-3-yl]oxy}-2-({[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-3-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol
Traditional IUPAC Name(2R,3R,4S,5S,6R)-2-{[(2R,3S,4R,5R,6R)-4,5-dihydroxy-6-{[(2R,3S,4R,5R,6S)-4,5,6-trihydroxy-2-(hydroxymethyl)oxan-3-yl]oxy}-2-({[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-3-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol
Chemical FormulaC24H42O21
SMILES[H]OC([H])([H])[C@@]1([H])O[C@]([H])(OC([H])([H])[C@@]2([H])O[C@]([H])(O[C@@]3([H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@@]([H])(O[H])O[C@]3([H])C([H])([H])O[H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@]2([H])O[C@@]2([H])O[C@]([H])(C([H])([H])O[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]2([H])O[H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@]1([H])O[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as oligosaccharides. These are carbohydrates made up of 3 to 10 monosaccharide units linked to each other through glycosidic bonds.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentOligosaccharides
Alternative Parents
Substituents
  • Oligosaccharide
  • O-glycosyl compound
  • Glycosyl compound
  • Oxane
  • Secondary alcohol
  • Hemiacetal
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Acetal
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting point270-280 °C
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility343 g/LALOGPS
logP-2.7ALOGPS
logP-8.2ChemAxon
logS-0.29ALOGPS
pKa (Strongest Acidic)11.19ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count21ChemAxon
Hydrogen Donor Count14ChemAxon
Polar Surface Area347.83 ŲChemAxon
Rotatable Bond Count10ChemAxon
Refractivity133.16 m³·mol⁻¹ChemAxon
Polarizability61.39 ųChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • vacuole
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Starch and sucrose metabolismPW002481 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Starch and sucrose metabolismec00500 Map00500
SMPDB Reactions
Amylose → Glycogen
Alpha-D-Glucose → Glycogen
Glycogen → Dextrin
Amylose → Glycogen + Alpha-D-Glucose
Glycogen + phosphate → Amylose + Glucose 1-phosphate
KEGG Reactions
amylose → Glycogen + water
Glycogen + water → D-Glucose
Glycogen + phosphate → Glucose 1-phosphate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000b-0401739000-7d2f2aaa7732e23ef9feJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0505921000-56fc10eb2d6cb63bc487JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0043-1906412000-81ae228fd873321b008cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0gbj-0400339000-de452d5dddd55d2855ffJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004s-3901435000-bc5da17144e98986d7b1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-4839321000-4dfca4172b8470e37b09JSpectraViewer
MSMass Spectrum (Electron Ionization)splash10-000j-1310429000-3dcc46e2d27cb731a1faJSpectraViewer | MoNA
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • 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
  • Teste, M. A., Enjalbert, B., Parrou, J. L., Francois, J. M. (2000). "The Saccharomyces cerevisiae YPR184w gene encodes the glycogen debranching enzyme." FEMS Microbiol Lett 193:105-110.11094287
  • Nookaew, I., Jewett, M. C., Meechai, A., Thammarongtham, C., Laoteng, K., Cheevadhanarak, S., Nielsen, J., Bhumiratana, S. (2008). "The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism." BMC Syst Biol 2:71.18687109
  • Wang, Z., Wilson, W. A., Fujino, M. A., Roach, P. J. (2001). "Antagonistic controls of autophagy and glycogen accumulation by Snf1p, the yeast homolog of AMP-activated protein kinase, and the cyclin-dependent kinase Pho85p." Mol Cell Biol 21:5742-5752.11486014
Synthesis Reference:Parodi A J; Krisman C R; Mordoh J In vitro synthesis of particulate glycogen from uridine diphosphate glucose. II. Some studies on the growth process. Archives of biochemistry and biophysics (1970), 141(1), 219-27.
External Links:
ResourceLink
CHEBI ID28087
HMDB IDHMDB00757
Pubchem Compound ID439177
Kegg IDC00182
ChemSpider ID388322
FOODB IDFDB022227
WikipediaGlycogen
BioCyc IDCPD0-971

Enzymes

Protein Details
1. Glucosidase 2 subunit alpha
General function:
Involved in catalytic activity
Specific function:
Catalytic subunit of glucosidase 2, which cleaves sequentially the 2 innermost alpha-1,3-linked glucose residues from the Glc(2)Man(9)GlcNAc(2) oligosaccharide precursor of immature glycoproteins
Gene Name:
ROT2
Uniprot ID:
P38138
Molecular weight:
110265.0
Reactions
Protein Details
2. Glycogen debranching enzyme
General function:
Involved in catalytic activity
Specific function:
Multifunctional enzyme acting as 1,4-alpha-D-glucan:1,4- alpha-D-glucan 4-alpha-D-glycosyltransferase and amylo-1,6- glucosidase in glycogen degradation
Gene Name:
GDB1
Uniprot ID:
Q06625
Molecular weight:
174970.0
Reactions
Protein Details
3. Glucoamylase, intracellular sporulation-specific
General function:
Involved in catalytic activity
Specific function:
Hydrolysis of terminal (1->4)-linked alpha-D- glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose
Gene Name:
SGA1
Uniprot ID:
P08019
Molecular weight:
61462.39844
Reactions
Protein Details
4. Glycogen phosphorylase
General function:
Involved in phosphorylase activity
Specific function:
Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties
Gene Name:
GPH1
Uniprot ID:
P06738
Molecular weight:
103274.0
Reactions
(1,4-alpha-D-glucosyl)(n) + phosphate → (1,4-alpha-D-glucosyl)(n-1) + alpha-D-glucose 1-phosphate.
Protein Details
5. Glycogen [starch] synthase isoform 2
General function:
Involved in glycogen (starch) synthase activity
Specific function:
Transfers the glycosyl residue from UDP-Glc to the non- reducing end of alpha-1,4-glucan. Is believed to regulate the synthesis of glycogen
Gene Name:
GSY2
Uniprot ID:
P27472
Molecular weight:
80078.20313
Reactions
UDP-glucose ((1->4)-alpha-D-glucosyl)(n) → UDP + ((1->4)-alpha-D-glucosyl)(n+1).
Protein Details
6. Glycogen [starch] synthase isoform 1
General function:
Involved in glycogen (starch) synthase activity
Specific function:
Transfers the glycosyl residue from UDP-Glc to the non- reducing end of alpha-1,4-glucan. Is believed to regulate the synthesis of glycogen
Gene Name:
GSY1
Uniprot ID:
P23337
Molecular weight:
80509.60156
Reactions
UDP-glucose ((1->4)-alpha-D-glucosyl)(n) → UDP + ((1->4)-alpha-D-glucosyl)(n+1).
Protein Details
7. 1,4-alpha-glucan-branching enzyme
General function:
Involved in catalytic activity
Specific function:
Transfers a segment of a (1->4)-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain
Gene Name:
GLC3
Uniprot ID:
P32775
Molecular weight:
81114.89844
Reactions