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Glycogen (YMDB00881)

Identification
YMDB IDYMDB00881
NameGlycogen
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionGlycogen is a polysaccharide that is the principal storage form of glucose in animal and human cells.
Structure
Thumb
ZoomMOLSDFPDBSMILESInChIView Structure
Synonyms
  • Glycogen
  • Lyoglycogen
  • Phytoglycogen
CAS number9005-79-2
WeightAverage: 666.5777
Monoisotopic: 666.221858406
InChI KeyInChIKey=BYSGBSNPRWKUQH-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(2S,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}-3-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol
Traditional IUPAC Name(2S,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}-3-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]methoxy}-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
KingdomOrganic Compounds
Super ClassCarbohydrates and Carbohydrate Conjugates
ClassTetrasaccharides
Sub ClassHexose Tetrasaccharides
Other Descriptors
  • Organic Oxonium Compounds
  • Aliphatic Heteropolycyclic Compounds
Substituents
  • Organic Oxonium Compounds
  • Aliphatic Heteropolycyclic Compounds
Physical Properties
StateSolid
Charge0
Melting point270-280 °C
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility343.0ALOGPS
logP-2.7ALOGPS
logP-8.2ChemAxon
logS-0.29ALOGPS
Hydrogen Acceptor Count21ChemAxon
Hydrogen Donor Count14ChemAxon
Polar Surface Area347.83 Å2ChemAxon
Rotatable Bond Count10ChemAxon
Refractivity133.16 m3·mol-1ChemAxon
Polarizability60.46 Å3ChemAxon
Biological Properties
Cellular Locations
  • vacuole
  • cytoplasm
PathwaysNot Available
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra1D NMR2D NMR
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 ID:28087
HMDB ID:HMDB00757
Pubchem Compound ID:439177
Kegg ID:C00182
Wikipedia:Glycogen
BioCyc ID:CPD0-971

Enzymes

Protein Details
1. 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
Transfers a segment of a (1->4)-alpha-D-glucan to a new position in an acceptor, which may be glucose or a (1->4)-alpha-D-glucan.
Hydrolysis of (1->6)-alpha-D-glucosidic branch linkages in glycogen phosphorylase limit dextrin.
Protein Details
2. 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
Hydrolysis of terminal (1->4)-linked alpha-D-glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose.
Protein Details
3. 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
4. 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
5. 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
6. 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
Transfers a segment of a (1->4)-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain.