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Glycine (YMDB00016)

Identification
YMDB IDYMDB00016
NameGlycine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionGlycine (abbreviated as Gly or G) is an alpha-amino acid. It is one of the 22 proteinogenic amino acids, i.e., the building blocks of proteins. It is the smallest, simplest amino acid as it lacks any side chain or chirality. It is generally considered a polar amino acid. Glycine is a colourless, sweet-tasting crystalline solid. The principal function of glycine is as a precursor to proteins. It is also a building block to numerous natural products. Glycine is classified as a glucogenic amino acid, since it can be converted to serine by serine hydroxymethyltransferase, and serine can be converted back to the glycolytic intermediate, 3-phosphoglycerate or to pyruvate by serine/threonine dehydratase. Glycine is degraded via three pathways. The predominant pathway involves the catalysis of glycine cleavage enzyme, the same enzyme also involved in the biosynthesis of glycine. In the second pathway, glycine is degraded in two steps. The first step is the reverse of glycine biosynthesis from serine with serine hydroxymethyl transferase. Serine is then converted to pyruvate by serine dehydratase. In the third pathway, glycine is converted to glyoxylate by D-amino acid oxidase.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 2-Aminoacetate
  • 2-Aminoacetic acid
  • Acid, aminoacetic
  • Aciport
  • amino-Acetate
  • amino-Acetic acid
  • Aminoacetate
  • Aminoacetic acid
  • Aminoessigsaeure
  • Aminoethanoate
  • Aminoethanoic acid
  • Calcium salt glycine
  • Cobalt salt glycine
  • Copper salt glycine
  • G
  • Glicoamin
  • Gly
  • Glycin
  • Glycine carbonate (1:1), monosodium salt
  • Glycine carbonate (2:1), monolithium salt
  • Glycine carbonate (2:1), monopotassium salt
  • Glycine carbonate (2:1), monosodium salt
  • Glycine hydrochloride
  • Glycine hydrochloride (2:1)
  • Glycine phosphate
  • Glycine phosphate (1:1)
  • Glycine sulfate (3:1)
  • Glycine, calcium salt
  • Glycine, calcium salt (2:1)
  • Glycine, cobalt salt
  • Glycine, copper salt
  • Glycine, monoammonium salt
  • Glycine, monopotasssium salt
  • Glycine, monosodium salt
  • Glycine, sodium hydrogen carbonate
  • Glycocoll
  • Glycolixir
  • Glycosthene
  • Glykokoll
  • Glyzin
  • Gyn-Hydralin
  • H2N-CH2-COOH
  • Hgly
  • Hydrochloride, glycine
  • Leimzucker
  • Monoammonium salt glycine
  • Monopotasssium salt glycine
  • Monosodium salt glycine
  • Padil
  • Phosphate, glycine
  • Salt glycine, monoammonium
  • Salt glycine, monosodium
CAS number56-40-6
WeightAverage: 75.0666
Monoisotopic: 75.032028409
InChI KeyDHMQDGOQFOQNFH-UHFFFAOYSA-N
InChIInChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)
IUPAC Name2-aminoacetic acid
Traditional IUPAC Nameglycine
Chemical FormulaC2H5NO2
SMILES[H]OC(=O)C([H])([H])N([H])[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids
Alternative Parents
Substituents
  • Alpha-amino acid
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organic nitrogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Primary aliphatic amine
  • Organic oxygen compound
  • Carbonyl group
  • Amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting point262.2 °C
Experimental Properties
PropertyValueReference
Water Solubility249 mg/mL at 25 oC [YALKOWSKY,SH & DANNENFELSER,RM (1992)]PhysProp
LogP-3.21 [HANSCH,C ET AL. (1995)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility552 g/LALOGPS
logP-3.3ALOGPS
logP-3.4ChemAxon
logS0.87ALOGPS
pKa (Strongest Acidic)2.31ChemAxon
pKa (Strongest Basic)9.24ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area63.32 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity16 m³·mol⁻¹ChemAxon
Polarizability6.65 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • extracellular
  • mitochondrion
  • cytoplasm
Organoleptic Properties
Flavour/OdourSource
OdorlessFDB000484
SMPDB Pathways
Glutathione metabolismPW002395 ThumbThumb?image type=greyscaleThumb?image type=simple
Nitrogen metabolismPW002504 ThumbThumb?image type=greyscaleThumb?image type=simple
One Carbon Pool by Folate IPW002468 ThumbThumb?image type=greyscaleThumb?image type=simple
Porphyrin MetabolismPW002462 ThumbThumb?image type=greyscaleThumb?image type=simple
glycine metabolismPW002398 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Cyanoamino acid metabolismec00460 Map00460
Glutathione metabolismec00480 Map00480
Glycine, serine and threonine metabolismec00260 Map00260
Lysine degradationec00310 Map00310
Methane metabolismec00680 Map00680
SMPDB Reactions
Gamma-Glutamylcysteine + Glycine + Adenosine triphosphate → ADP + phosphate + hydron + Glutathione
L-cysteinylglycine + water → Glycine + L-Cysteine
L-Serine + Tetrahydrofolic acid → water + Glycine + 5,10-Methylene-THF
L-Serine + Tetrahydrofolic acid → water + Glycine + 5,10-Methylene-THF
Glycine + Tetrahydrofolic acid → Ammonium + 5,10-Methylene-THF
KEGG Reactions
Glycine + hydron + Succinyl-CoA → 5-Aminolevulinic acid + Carbon dioxide + Coenzyme A
Glyoxylic acid + L-Alanine → Pyruvic acid + Glycine
Adenosine triphosphate + Glycine + Gamma-Glutamylcysteine → phosphate + Glutathione + hydron + ADP
L-2-amino-3-oxobutanoic acid + Coenzyme A → Glycine + Acetyl-CoA
NAD + Glycine + 5,6,7,8-Tetrahydrofolic acid → NADH + Carbon dioxide + 5,10-Methylene-THF + Ammonium
Concentrations
Intracellular Concentrations
Intracellular ConcentrationSubstrateGrowth ConditionsStrainCitation
3279 ± 65 µM YPD mediaaerobicBaker's yeastPMID: 7654310
1093 ± 22 µM YPG mediaaerobicBaker's yeastPMID: 7654310
2869 ± 57 µM SD mediaaerobicBaker's yeastPMID: 7654310
1366 ± 27 µM SG mediaaerobicBaker's yeastPMID: 7654310
3142 ± 63 µM M (molasses)aerobicBaker's yeastPMID: 7654310
7241 ± 145 µM MA (molasses)aerobicBaker's yeastPMID: 7654310
3006 ± 60 µM MB (molasses)aerobicBaker's yeastPMID: 7654310
4782 ± 96 µM MAB (molasses)aerobicBaker's yeastPMID: 7654310
1291 ± 65 µM YEB media with 0.5 mM glucoseaerobicBaker's yeastExperimentally Determined
Not Available
780 ± 287 µM Synthetic medium with 20 g/L glucoseaerobicBaker's yeastPMID: 12584756
15000 ± 0 µM Minimal medium supplemented with glucoseaerobic;resting cellsBaker's yeastPMID: 4578278
15000 ± 0 µM Minimal medium supplemented with ammonium and glucoseaerobic;growing cellsBaker's yeastPMID: 4578278
Conversion Details Here
Extracellular Concentrations
Intracellular ConcentrationSubstrateGrowth ConditionsStrainCitation
1732 ± 0 µM hops, malted barleyanaerobicBaker's yeastAlcoholic beverage, beer, regular, all - U.S. Department of Agriculture, Agricultural Research Service. 2010. USDA National Nutrient Database for Standard Reference, Release 23. Nutrient Data Laboratory Home Page
Conversion Details Here
Spectra
Spectra
References
References:
  • Martinez-Force, E., Benitez, T. (1995). "Effects of varying media, temperature, and growth rates on the intracellular concentrations of yeast amino acids." Biotechnol Prog 11:386-392.7654310
  • 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
  • Flynn, N. E., Patyrak, M. E., Seely, J. B., Wu, G. (2010). "Glycine oxidation and conversion into amino acids in Saccharomyces cerevisiae and Candida albicans." Amino Acids 39:605-608.20091413
  • Chelstowska, A., Rytka, J. (1993). "[Biosynthesis of heme in yeast Saccharomyces cerevisiae]." Postepy Biochem 39:173-185.8234090
  • Takada, Y., Noguchi, T. (1985). "Characteristics of alanine: glyoxylate aminotransferase from Saccharomyces cerevisiae, a regulatory enzyme in the glyoxylate pathway of glycine and serine biosynthesis from tricarboxylic acid-cycle intermediates." Biochem J 231:157-163.3933486
  • Alcoholic beverage, beer, regular, all - U.S. Department of Agriculture, Agricultural Research Service. 2010. USDA National Nutrient Database for Standard Reference, Release 23. Nutrient Data Laboratory Home Page
  • Hans, M. A., Heinzle, E., Wittmann, C. (2003). "Free intracellular amino acid pools during autonomous oscillations in Saccharomyces cerevisiae." Biotechnol Bioeng 82:143-151.12584756
  • Schreve, J. L., Sin, J. K., Garrett, J. M. (1998). "The Saccharomyces cerevisiae YCC5 (YCL025c) gene encodes an amino acid permease, Agp1, which transports asparagine and glutamine." J Bacteriol 180:2556-2559.9573211
  • 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
  • McNeil, J. B., Bognar, A. L., Pearlman, R. E. (1996). "In vivo analysis of folate coenzymes and their compartmentation in Saccharomyces cerevisiae." Genetics 142:371-381.8852837
  • Turner, R. J., Lovato, M., Schimmel, P. (2000). "One of two genes encoding glycyl-tRNA synthetase in Saccharomyces cerevisiae provides mitochondrial and cytoplasmic functions." J Biol Chem 275:27681-27688.10874035
  • Liu, J. Q., Nagata, S., Dairi, T., Misono, H., Shimizu, S., Yamada, H. (1997). "The GLY1 gene of Saccharomyces cerevisiae encodes a low-specific L-threonine aldolase that catalyzes cleavage of L-allo-threonine and L-threonine to glycine--expression of the gene in Escherichia coli and purification and characterization of the enzyme." Eur J Biochem 245:289-293.9151955
  • Gancedo, J. M., Gancedo, C. (1973). "Concentrations of intermediary metabolites in yeast." Biochimie 55:205-211.4578278
  • 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: Anslow, Winston K.; King, Harold. Synthesis of glycine. Journal of the Chemical Society (1929), 2163-6.
External Links:
ResourceLink
CHEBI ID15428
HMDB IDHMDB00123
Pubchem Compound ID750
Kegg IDC00037
ChemSpider ID730
FOODB IDFDB000484
WikipediaGlycine
BioCyc IDGLY

Enzymes

Protein Details
1. Glycine dehydrogenase [decarboxylating], mitochondrial
General function:
Involved in glycine dehydrogenase (decarboxylating) activity
Specific function:
The glycine cleavage system (glycine decarboxylase complex) catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein
Gene Name:
GCV2
Uniprot ID:
P49095
Molecular weight:
114450.0
Reactions
Glycine + H-protein-lipoyllysine → H-protein-S-aminomethyldihydrolipoyllysine + CO(2).
Protein Details
2. Glutathione synthetase
General function:
Involved in ATP binding
Specific function:
ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione
Gene Name:
GSH2
Uniprot ID:
Q08220
Molecular weight:
55814.69922
Reactions
ATP + gamma-L-glutamyl-L-cysteine + glycine → ADP + phosphate + glutathione.
Protein Details
3. Serine hydroxymethyltransferase, cytosolic
General function:
Involved in catalytic activity
Specific function:
Interconversion of serine and glycine
Gene Name:
SHM2
Uniprot ID:
P37291
Molecular weight:
52218.0
Reactions
5,10-methylenetetrahydrofolate + glycine + H(2)O → tetrahydrofolate + L-serine.
Protein Details
4. Serine hydroxymethyltransferase, mitochondrial
General function:
Involved in catalytic activity
Specific function:
Interconversion of serine and glycine
Gene Name:
SHM1
Uniprot ID:
P37292
Molecular weight:
53686.0
Reactions
5,10-methylenetetrahydrofolate + glycine + H(2)O → tetrahydrofolate + L-serine.
Protein Details
5. Low specificity L-threonine aldolase
General function:
Involved in lyase activity
Specific function:
Catalyzes the cleavage of L-allo-threonine and L- threonine to glycine and acetaldehyde
Gene Name:
GLY1
Uniprot ID:
P37303
Molecular weight:
42814.60156
Reactions
L-threonine → glycine + acetaldehyde.
L-allo-threonine → glycine + acetaldehyde.
Protein Details
6. 5-aminolevulinate synthase, mitochondrial
General function:
Involved in 5-aminolevulinate synthase activity
Specific function:
Succinyl-CoA + glycine = 5-aminolevulinate + CoA + CO(2)
Gene Name:
HEM1
Uniprot ID:
P09950
Molecular weight:
59361.69922
Reactions
Succinyl-CoA + glycine → 5-aminolevulinate + CoA + CO(2).
Protein Details
7. Alanine--glyoxylate aminotransferase 1
General function:
Involved in metabolic process
Specific function:
Has alanine:glyoxylate aminotransferase activity
Gene Name:
AGX1
Uniprot ID:
P43567
Molecular weight:
41906.80078
Reactions
L-alanine + glyoxylate → pyruvate + glycine.
Protein Details
8. Glycyl-tRNA synthetase 1
General function:
Involved in nucleotide binding
Specific function:
Catalyzes the attachment of glycine to tRNA(Gly). Is also able produce diadenosine tetraphosphate (Ap4A), a universal pleiotropic signaling molecule needed for cell regulation pathways, by direct condensation of 2 ATPs
Gene Name:
GRS1
Uniprot ID:
P38088
Molecular weight:
75410.20313
Reactions
ATP + glycine + tRNA(Gly) → AMP + diphosphate + glycyl-tRNA(Gly).
Protein Details
9. Bifunctional purine biosynthetic protein ADE5,7
General function:
Involved in catalytic activity
Specific function:
ATP + 5-phospho-D-ribosylamine + glycine = ADP + phosphate + N(1)-(5-phospho-D-ribosyl)glycinamide
Gene Name:
ADE5
Uniprot ID:
P07244
Molecular weight:
86067.39844
Reactions
ATP + 5-phospho-D-ribosylamine + glycine → ADP + phosphate + N(1)-(5-phospho-D-ribosyl)glycinamide.
ATP + 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine → ADP + phosphate + 5-amino-1-(5-phospho-D-ribosyl)imidazole.
Protein Details
10. Glycyl-tRNA synthetase 2
General function:
Involved in nucleotide binding
Specific function:
Catalyzes the attachment of glycine to tRNA(Gly). Is also able produce diadenosine tetraphosphate (Ap4A), a universal pleiotropic signaling molecule needed for cell regulation pathways, by direct condensation of 2 ATPs
Gene Name:
GRS2
Uniprot ID:
Q06817
Molecular weight:
71017.89844
Reactions
ATP + glycine + tRNA(Gly) → AMP + diphosphate + glycyl-tRNA(Gly).
Protein Details
11. Dihydrolipoyl dehydrogenase, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
Lipoamide dehydrogenase is a component of the alpha- ketoacid dehydrogenase complexes. This includes the pyruvate dehydrogenase complex, which catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). Acts also as component of the glycine cleavage system (glycine decarboxylase complex), which catalyzes the degradation of glycine
Gene Name:
LPD1
Uniprot ID:
P09624
Molecular weight:
54009.69922
Reactions
Protein N(6)-(dihydrolipoyl)lysine + NAD(+) → protein N(6)-(lipoyl)lysine + NADH.
Protein Details
12. Serine palmitoyltransferase 1
General function:
Involved in transferase activity, transferring nitrogenous groups
Specific function:
Component of serine palmitoyltransferase (SPT), which catalyzes the committed step in the synthesis of sphingolipids, the condensation of serine with palmitoyl CoA to form the long chain base 3-ketosphinganine
Gene Name:
LCB1
Uniprot ID:
P25045
Molecular weight:
62206.60156
Reactions
Palmitoyl-CoA + L-serine → CoA + 3-dehydro-D-sphinganine + CO(2).
Protein Details
13. Aminomethyltransferase, mitochondrial
General function:
Involved in aminomethyltransferase activity
Specific function:
The glycine cleavage system (glycine decarboxylase complex) catalyzes the degradation of glycine
Gene Name:
GCV1
Uniprot ID:
P48015
Molecular weight:
44468.69922
Reactions
[Protein]-S(8)-aminomethyldihydrolipoyllysine + tetrahydrofolate → [protein]-dihydrolipoyllysine + 5,10-methylenetetrahydrofolate + NH(3).

Transporters

Protein Details
1. General amino-acid permease GAP1
General function:
Involved in transport
Specific function:
Permease for various amino acids as well as for GABA. Can also transport L-cysteine and beta-alanine
Gene Name:
GAP1
Uniprot ID:
P19145
Molecular weight:
65654.89844
Protein Details
2. Dicarboxylic amino acid permease
General function:
Involved in transport
Specific function:
Can transport glutamate, aspartate, glutamine, asparagine, serine, alanine and glycine
Gene Name:
DIP5
Uniprot ID:
P53388
Molecular weight:
68096.70313
Protein Details
3. Proline-specific permease
General function:
Involved in transport
Specific function:
Required for high-affinity proline transport. May be responsible for proline recognition and probably also for proline translocation across the plasma membrane. Also function as non- specific GABA permease. Can also transport alanine and glycine
Gene Name:
PUT4
Uniprot ID:
P15380
Molecular weight:
68786.79688
Protein Details
4. Tryptophan permease
General function:
Involved in transport
Specific function:
Required for high-affinity tryptophan transport. Also transports cysteine, phenyalanine and tyrosine
Gene Name:
TAT2
Uniprot ID:
P38967
Molecular weight:
65403.80078
Protein Details
5. General amino acid permease AGP1
General function:
Involved in transport
Specific function:
Broad substrate range permease which transports asparagine and glutamine with intermediate specificity. Also transports Ala, Cys, Gly, Ile, Leu, Met, Phe, Ser, Thr, Tyr and Val. Important for the utilization of amino acids as a nitrogen source
Gene Name:
AGP1
Uniprot ID:
P25376
Molecular weight:
69670.70313