Glycogen (YMDB00881)

Identification

YMDB ID

YMDB00881

Name

Glycogen

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Glycogen, 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

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms

Glycogen
Lyoglycogen
Phytoglycogen
Animal starch
Liver starch

CAS number

9005-79-2

Weight

Average: 666.5777
Monoisotopic: 666.221858406

InChI Key

BYSGBSNPRWKUQH-UJDJLXLFSA-N

InChI

InChI=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

Chemical Formula

C₂₄H₄₂O₂₁

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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Oligosaccharides

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 Framework

Aliphatic heteromonocyclic compounds

External Descriptors

glycogens (CHEBI:28087 )

Physical Properties

State

Solid

Charge

Melting point

270-280 °C

Experimental Properties

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

Predicted Properties

Property	Value	Source
Water Solubility	343 g/L	ALOGPS
logP	-2.7	ALOGPS
logP	-8.2	ChemAxon
logS	-0.29	ALOGPS
pKa (Strongest Acidic)	11.19	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	21	ChemAxon
Hydrogen Donor Count	14	ChemAxon
Polar Surface Area	347.83 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	133.16 m³·mol⁻¹	ChemAxon
Polarizability	61.39 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

vacuole
cytoplasm

Organoleptic Properties

Not Available

SMPDB Pathways

Starch and sucrose metabolism

PW002481

KEGG Pathways

Starch and sucrose metabolism

ec00500

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 Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_7) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_8) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_9) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_10) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_11) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_12) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_13) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_14) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, Positive	Not Available	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000b-0401739000-7d2f2aaa7732e23ef9fe	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-0505921000-56fc10eb2d6cb63bc487	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0043-1906412000-81ae228fd873321b008c	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0gbj-0400339000-de452d5dddd55d2855ff	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004s-3901435000-bc5da17144e98986d7b1	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-4839321000-4dfca4172b8470e37b09	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-066r-0100029000-b6e0ee6c4d7da972d403	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0cfr-8200197000-418a1a524982d51ac37c	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-052o-9112031000-54aa8775ffd121394c79	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014j-0000219000-3e1e676b7e59ddc5e400	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0ap1-1202269000-46a5b5753a69d2459f1c	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00mp-9105250000-f7a96871cd5435e63e92	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H 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:

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:

Resource	Link
CHEBI ID	28087
HMDB ID	HMDB00757
Pubchem Compound ID	439177
Kegg ID	C00182
ChemSpider ID	388322
FOODB ID	FDB022227
Wikipedia	Glycogen
BioCyc ID	CPD0-971

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

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Structure for #<Compound:0xaad473bc>

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