Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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MetaCyc Compound: glycine

Abbrev Name: gly

Synonyms: G, aminoacetic acid, gly

Superclasses: an amino acid or its derivative an amino acid a neutral amino acid
an amino acid or its derivative an amino acid a non-polar amino acid
an amino acid or its derivative an amino acid a polar amino acid an uncharged polar amino acid
an amino acid or its derivative an amino acid an alpha amino acid a standard alpha amino acid

Chemical Formula: C2H5NO2

Molecular Weight: 75.067 Daltons

Monoisotopic Molecular Weight: 75.0320284099 Daltons

SMILES: C([N+])C([O-])=O

InChI: InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)

InChIKey: InChIKey=DHMQDGOQFOQNFH-UHFFFAOYSA-N

Unification Links: CAS:56-40-6 , ChEBI:15428 , ChemSpider:730 , DrugBank:DB00145 , HMDB:HMDB00123 , IAF1260:33610 , KEGG:C00037 , KNApSAcK:C00001361 , MetaboLights:MTBLC15428 , PubChem:5257127

Standard Gibbs Free Energy of Change Formation (ΔfG in kcal/mol): -37.2444 Inferred by computational analysis [Latendresse13]

Reactions known to consume the compound:

2-amino-3-hydroxycyclopent-2-enone biosynthesis , tetrapyrrole biosynthesis II (from glycine) :
glycine + succinyl-CoA + H+ → CO2 + 5-aminolevulinate + coenzyme A

5-aminoimidazole ribonucleotide biosynthesis I , 5-aminoimidazole ribonucleotide biosynthesis II , superpathway of 5-aminoimidazole ribonucleotide biosynthesis :
5-phospho-β-D-ribosylamine + ATP + glycine → ADP + N1-(5-phospho-β-D-ribosyl)glycinamide + phosphate + H+

bacillibactin biosynthesis :
3 2,3-dihydroxybenzoate + 3 glycine + 3 L-threonine + 6 ATP → bacillibactin + 6 AMP + 6 diphosphate + 3 H+ + 3 H2O

bile acid biosynthesis, neutral pathway :
choloyl-CoA + glycine → glycocholate + coenzyme A + H+
chenodeoxycholoyl-CoA + glycine → glycochenodeoxycholate + coenzyme A + H+

bupropion degradation :
3-chlorobenzoate + glycine → m-chlorohippurate + H2O

butanol and isobutanol biosynthesis (engineered) :
glycine + oxygen + H2O → ammonium + hydrogen peroxide + glyoxylate

creatine biosynthesis :
glycine + L-arginine → guanidinoacetate + L-ornithine

glutathione biosynthesis :
glycine + γ-L-glutamyl-L-cysteine + ATP → glutathione + ADP + phosphate + H+

glycine betaine biosynthesis IV (from glycine) , glycine betaine biosynthesis V (from glycine) :
S-adenosyl-L-methionine + glycineS-adenosyl-L-homocysteine + sarcosine + H+

glycolate and glyoxylate degradation III :
(3R)-3-hydroxy-L-aspartate ← glycine + glyoxylate

phenylalanine degradation IV (mammalian, via side chain) :
phenylacetyl-CoA + glycine → phenylacetylglycine + coenzyme A + H+

purine nucleobases degradation I (anaerobic) :
acetyl phosphate + ammonium + an oxidized thioredoxin + H2O ← glycine + a reduced thioredoxin + phosphate + H+

pyruvate fermentation to opines :
strombine + NAD+ + H2O ← pyruvate + glycine + NADH + H+

thiazole biosynthesis II (Bacillus) :
glycine + oxygen → 2-iminoacetate + hydrogen peroxide + H+

thiazole biosynthesis III (eukaryotes) :
glycine + L-cysteine + NAD+ → 2-carboxylate-4-methyl-5-beta-(ethyl adenosine 5-diphosphate) thiazole + nicotinamide + L-alanine + 3 H2O

tRNA charging :
tRNAgly + glycine + ATP + H+ → glycyl-tRNAgly + AMP + diphosphate

Not in pathways:
benzoyl-CoA + glycine → hippurate + coenzyme A + H+
2 S-adenosyl-L-methionine + glycine → 2 S-adenosyl-L-homocysteine + dimethylglycine + 2 H+
3 S-adenosyl-L-methionine + glycine → 3 S-adenosyl-L-homocysteine + glycine betaine + 3 H+
indole-3-acetate + glycine + ATP → indole-3-acetyl-glycine + AMP + diphosphate + H+

γ-glutamyl cycle :
glutathione + a standard α amino acid → L-cysteinyl-glycine + an (γ-L-glutamyl)-L-amino acid

leukotriene biosynthesis :
leukotriene-C4 + a standard α amino acid → an (γ-L-glutamyl)-L-amino acid + leukotriene-D4

methanofuran biosynthesis :
2-furaldehyde phosphate + a standard α amino acid → 2-methylamine-furan phosphate + a 2-oxo carboxylate


a standard α amino acid + oxygen + H2O → ammonium + hydrogen peroxide + a 2-oxo carboxylate

Reactions known to produce the compound:

2-aminoethylphosphonate degradation III :
(2-amino-1-hydroxyethyl)phosphonate + oxygen → glycine + phosphate + 2 H+

4-hydroxy-2-nonenal detoxification :
4-hydroxy-2-nonenal-[Cys-Gly] conjugate + H2O → 4-hydroxy-2-nonenal-[L-Cys] conjugate + glycine

camalexin biosynthesis :
indole-3-acetonitrile-glutatione conjugate + H2O → indole-3-acetonitrile-γ-glutamylcysteine conjugate + glycine

creatinine degradation I :
sarcosine + oxygen + H2O → glycine + formaldehyde + hydrogen peroxide
sarcosine + an oxidized electron-transfer flavoprotein + H2O + H+glycine + formaldehyde + a reduced electron-transfer flavoprotein

creatinine degradation II :
sarcosine + oxygen + H2O → glycine + formaldehyde + hydrogen peroxide
sarcosine + an oxidized electron-transfer flavoprotein + H2O + H+glycine + formaldehyde + a reduced electron-transfer flavoprotein

γ-glutamyl cycle , glutathione degradation (DUG pathway - yeast) :
L-cysteinyl-glycine + H2O → L-cysteine + glycine

gliotoxin biosynthesis :
3-benzyl-3,6 -bis(cysteinylglycine)- 6-(hydroxymethyl)-diketopiperazine + 2 H2O → 3-benzyl-3,6 -bis(cysteinyl)- 6-(hydroxymethyl)-diketopiperazine + 2 glycine

glutathione-mediated detoxification I :
a [Cys-Gly]-S-conjugate + H2O → an L-cysteine-S-conjugate + glycine

glutathione-mediated detoxification II :
a [Cys-Gly]-S-conjugate + H2O → an L-cysteine-S-conjugate + glycine
a glutathione-toxin conjugate + H2O → a [Glu-Cys]-S-conjugate + glycine

glycine betaine degradation I :
sarcosine + oxygen + H2O → glycine + formaldehyde + hydrogen peroxide

glycine betaine degradation II (mammalian) :
sarcosine + an oxidized electron-transfer flavoprotein + a tetrahydrofolate → glycine + a 5,10-methenyltetrahydrofolate + a reduced electron-transfer flavoprotein

glycine biosynthesis IV , threonine degradation IV :
L-threonine → acetaldehyde + glycine

glycocholate metabolism (bacteria) :
glycocholate + H2O → cholate + glycine

homophytochelatin biosynthesis :
glutathione + homoglutathione → γ-Glu-Cys-γ-Glu-Cys-β-Ala + glycine

indole glucosinolate breakdown (active in intact plant cell) :
indol-3-ylmethylisothiocyanate-glutathione + 2 H2O → 3-aminomethylindole + raphanusamic acid + L-glutamate + glycine
4-methoxy-3-indolylmethylisothiocyanate-glutathione + 2 H2O → 4-methoxy-3-indolylmethylamine + raphanusamic acid + L-glutamate + glycine

L-carnitine biosynthesis :
3-hydroxy-N6,N6,N6-trimethyl-L-lysine → 4-trimethylammoniobutanal + glycine

leukotriene biosynthesis :
leukotriene-D4 + H2O → glycine + leukotriene-E4

nitrilotriacetate degradation :
iminodiacetate + H2O → glycine + glyoxylate + 2 H+

phytochelatins biosynthesis :
[Glu(-Cys)]n-Gly + glutathione → [Glu(-Cys)](n+1)-Gly + glycine

Not in pathways:
a C-terminal [protein]-glycine + H2O → glycine + a peptide
glycyl-L-methionine + H2O → glycine + L-methionine
L-alanyl-glycine + H2O → L-alanine + glycine
glycyl-L-asparagine + H2O → glycine + L-asparagine
glycyl-L-glutamine + H2O → glycine + L-glutamine
glycyl-L-glutamate + H2O → glycine + L-glutamate
glycyl-L-aspartate + H2O → glycine + L-aspartate
glycyl-L-proline + H2O → glycine + L-proline
a protein with LPXTG motif + a pentaglycine cross-bridge of peptidoglycan + H2O → a protein with LPXT - pentaglycine cross-bridge of peptidoglycan + glycine
a protein with NXTN motif + a pentaglycine cross-bridge of peptidoglycan + H2O → a protein with NXTN - pentaglycine cross-bridge of peptidoglycan + glycine
hippurate + H2O → glycine + benzoate

dimethylsulfoniopropionate biosynthesis I (Wollastonia) :
S-methyl-L-methionine + a 2-oxo carboxylate + H+ → 3-dimethylsulfoniopropionaldehyde + CO2 + a standard α amino acid

seed germination protein turnover , wound-induced proteolysis I :
amino acids(n) + H2O → a standard α amino acid + amino acids(n-1)


a dipeptide + H2O → 2 amino acids
amino acids(n) + H2O → amino acids(n-1) + a standard α amino acid
β-aspartyl dipeptide + H2O → L-aspartate + a standard α amino acid
amino acids(n) + H2O → amino acids(n-1) + a standard α amino acid
a protein + H2O → a peptide + a standard α amino acid
a dipeptide + H2O → 2 a standard α amino acid
a peptide + H2O → a standard α amino acid + a peptide
a peptide + H2O → a peptide + a standard α amino acid
a peptide + H2O → a peptide + a standard α amino acid
an oligopeptide + H2O → a peptide + a standard α amino acid
a dipeptide + H2O → a standard α amino acid + a standard α amino acid
a protein + H2O → a peptide + a standard α amino acid
a protein + H2O → a peptide + a standard α amino acid
a protein + H2O → a standard α amino acid + a peptide
a peptide + H2O → a standard α amino acid + a peptide
a protein + H2O → a standard α amino acid + a peptide
a tripeptide + H2O → a dipeptide + a standard α amino acid
a dipetide with L-aspartate at the N-terminal + H2O → L-aspartate + a standard α amino acid
a dipetide with L-histidine at the C-terminal + H2O → a standard α amino acid + L-histidine
a dipeptide with L-methionine at the N-terminal + H2O → a standard α amino acid + L-methionine
a dipeptide with proline at the C-terminal + H2O → L-proline + a standard α amino acid
a dipeptide + H2O → a standard α amino acid + a standard α amino acid
a dipeptide + H2O → a standard α amino acid + a standard α amino acid
amino acids(n) + H2O → a standard α amino acid + amino acids(n-1)


an ester of hydrophobic-amino acids + H2O → a non-polar amino acid + a non-polar amino acid


amino acids(n) + H2O → amino acids(n-1) + an α amino acid
an α amino acid ester + H2O → an alcohol + an α amino acid + H+
a protein + H2O → a protein + an α amino acid

Reactions known to both consume and produce the compound:

folate polyglutamylation , glycine betaine degradation I , glycine betaine degradation II (mammalian) , glycine biosynthesis I :
L-serine + a tetrahydrofolate ↔ glycine + a 5,10-methylene-tetrahydrofolate + H2O

folate transformations I :
L-serine + a tetrahydrofolate ↔ glycine + a 5,10-methylene-tetrahydrofolate + H2O
glycine + a tetrahydrofolate + NAD+ ↔ a 5,10-methylene-tetrahydrofolate + ammonium + CO2 + NADH

folate transformations II :
L-serine + a tetrahydrofolate ↔ glycine + a 5,10-methylene-tetrahydrofolate + H2O
glycine + a tetrahydrofolate + NAD+ ↔ a 5,10-methylene-tetrahydrofolate + ammonium + CO2 + NADH

formaldehyde assimilation I (serine pathway) :
glyoxylate + L-serine ↔ hydroxypyruvate + glycine
glyoxylate + L-serine ↔ hydroxypyruvate + glycine
L-serine + a tetrahydrofolate ↔ glycine + a 5,10-methylene-tetrahydrofolate + H2O

glycine biosynthesis II , glycine cleavage :
glycine + a [glycine-cleavage complex H protein] N6-lipoyl-L-lysine + H+ ↔ a [glycine-cleavage complex H protein] N6-aminomethyldihydrolipoyl-L-lysine + CO2

glycine biosynthesis III :
glyoxylate + L-alanine ↔ glycine + pyruvate

N10-formyl-tetrahydrofolate biosynthesis :
L-serine + a tetrahydrofolate ↔ glycine + a 5,10-methylene-tetrahydrofolate + H2O
glycine + a tetrahydrofolate + NAD+ ↔ a 5,10-methylene-tetrahydrofolate + ammonium + CO2 + NADH

photorespiration :
glyoxylate + L-serine ↔ hydroxypyruvate + glycine
L-serine + a tetrahydrofolate ↔ glycine + a 5,10-methylene-tetrahydrofolate + H2O
glycine + a tetrahydrofolate + NAD+ ↔ a 5,10-methylene-tetrahydrofolate + ammonium + CO2 + NADH
2-oxoglutarate + glycine ↔ L-glutamate + glyoxylate

purine nucleobases degradation I (anaerobic) :
a 5-formiminotetrahydrofolate + glycineN-formimino-glycine + a tetrahydrofolate

purine nucleobases degradation II (anaerobic) :
L-serine + a tetrahydrofolate ↔ glycine + a 5,10-methylene-tetrahydrofolate + H2O
a 5-formiminotetrahydrofolate + glycineN-formimino-glycine + a tetrahydrofolate

threonine degradation II :
glycine + acetyl-CoA ↔ 2-amino-3-oxobutanoate + coenzyme A + H+

Not in pathways:
glyoxylate + L-methionine ↔ glycine + 2-oxo-4-methylthiobutanoate
L-kynurenine + glyoxylate ↔ glycine + 4-(2-aminophenyl)-2,4-dioxobutanoate
L-asparagine + glyoxylate ↔ 2-oxosuccinamate + glycine
4-hydroxy-L-threonine ↔ glycolaldehyde + glycine
glyoxylate + an aromatic amino acid ↔ glycine + an aromatic oxo-acid
L-allo-threonine ↔ glycine + acetaldehyde
4-aminobutanoate + glyoxylate ↔ succinate semialdehyde + glycine
DL-allothreonine ↔ acetaldehyde + glycine
oxaloacetate + glycine ↔ L-aspartate + glyoxylate

asparagine degradation II :
a 2-oxo carboxylate + L-asparagine ↔ 2-oxosuccinamate + a standard α amino acid

dimethylsulfoniopropionate biosynthesis III (algae) , ethylene biosynthesis III (microbes) :
L-methionine + a 2-oxo carboxylate ↔ 2-oxo-4-methylthiobutanoate + a standard α amino acid

glucosinolate biosynthesis from dihomomethionine :
2-oxo-6-methylthiohexanoate + a standard α amino acid ↔ L-dihomomethionine + a 2-oxo carboxylate

glucosinolate biosynthesis from hexahomomethionine :
2-oxo-10-methylthiodecanoate + a standard α amino acid ↔ hexahomomethionine + a 2-oxo carboxylate

glucosinolate biosynthesis from pentahomomethionine :
2-oxo-9-methylthiononanoate + a standard α amino acid ↔ pentahomomethionine + a 2-oxo carboxylate

glucosinolate biosynthesis from tetrahomomethionine :
2-oxo-8-methylthiooctanoate + a standard α amino acid ↔ tetrahomomethionine + a 2-oxo carboxylate

glucosinolate biosynthesis from trihomomethionine :
2-oxo-7-methylthioheptanoate + a standard α amino acid ↔ trihomomethionine + a 2-oxo carboxylate

homomethionine biosynthesis :
2-oxo-5-methylthiopentanoate + a standard α amino acid ↔ L-homomethionine + a 2-oxo carboxylate
L-methionine + a 2-oxo carboxylate ↔ 2-oxo-4-methylthiobutanoate + a standard α amino acid


L-ornithine + a 2-oxo carboxylate ↔ a standard α amino acid + L-glutamate-5-semialdehyde

In Reactions of unknown directionality:

homophytochelatin biosynthesis :
[Glu(-Cys)]n-β-Ala + glutathione = [Glu(-Cys)](n+1)-β-Ala + glycine

Not in pathways:
L-threo-3-phenylserine = benzaldehyde + glycine
(3S)-3-hydroxy-D-aspartate = glycine + glyoxylate
guanidinoacetate + H2O = urea + glycine
N-Benzyloxycarbonylglycine + H+ + H2O = glycine + CO2 + benzyl alcohol
N-feruloylglycine + H2O = ferulate + glycine
D-threonine = glycine + acetaldehyde
D-allothreonine = glycine + acetaldehyde
S-ureidoglycine + glyoxylate = oxalurate + glycine
(3R)-3-hydroxy-D-aspartate = glycine + glyoxylate
a tRNA uridine34 + GTP + a 5,10-methylene-tetrahydrofolate + glycine + H2O = a tRNA containing 5-carboxymethylaminomethyluridine + GDP + a 7,8-dihydrofolate + phosphate
a tRNA 2-thiouridine34 + GTP + glycine + a 5,10-methylene-tetrahydrofolate + H2O = a tRNA containing 5-carboxymethylaminomethyl-2-thiouridine + GDP + a 7,8-dihydrofolate + phosphate
2 an oxidized c-type cytochrome + glycine + H2O = 2 a reduced c-type cytochrome + ammonium + glyoxylate + 2 H+
(E)-cinnamoyl-CoA + glycine = cinnamoylglycine + coenzyme A + H+
3-phenylpropanoyl-CoA + glycine = N-(3-phenylpropanoyl)glycine + coenzyme A + H+
glycine + NAD+ + H2O = ammonium + glyoxylate + NADH + H+
glycine + ATP = glycyl-AMP + diphosphate
glycine + 2 acceptors = hydrogen cyanide + CO2 + 2 reduced acceptors
5,10-methylene-tetrahydromethanopterin + glycine + H2O = tetrahydromethanopterin + L-serine
an acyl-CoA + glycine = an N-acylglycine + coenzyme A


a 5-L-glutamyl-[peptide] + an amino acid = a 5-L-glutamyl-amino acid + a peptide

In Transport reactions:
2 glycine[out] + 2 H+[out] ↔ 2 glycine[in] + 2 H+[in] ,
glycine[periplasmic space]glycine[cytosol] ,
glycine[periplasmic space] + H+[periplasmic space]glycine[cytosol] + H+[cytosol] ,
a polar amino acid[extracellular space] + ATP + H2O ↔ a polar amino acid[cytosol] + ADP + phosphate ,
a non-polar amino acid[extracellular space] + ATP + H2O ↔ a non-polar amino acid[cytosol] + ADP + phosphate

Enzymes activated by glycine, sorted by the type of activation, are:

Activator (Allosteric) of: phosphoenolpyruvate carboxylase

Activator (Mechanism unknown) of: glutamate dehydrogenase (NAD-dependent) [Bonete96]

Enzymes inhibited by glycine, sorted by the type of inhibition, are:

Inhibitor (Competitive) of: serine acetyltransferase [Hindson03]

Inhibitor (Allosteric) of: α-ketoglutarate reductase [Zhao96] , D-3-phosphoglycerate dehydrogenase [Zhao96, Dubrow77, Sugimoto68a]

Inhibitor (Mechanism unknown) of: glutamine synthetase [Woolfolk67, Comment 1] , formyltetrahydrofolate deformylase [Nagy95]


References

Bonete96: Bonete MJ, Perez-Pomares F, Ferrer J, Camacho ML (1996). "NAD-glutamate dehydrogenase from Halobacterium halobium: inhibition and activation by TCA intermediates and amino acids." Biochim Biophys Acta 1996;1289(1);14-24. PMID: 8605224

Dubrow77: Dubrow R, Pizer LI (1977). "Transient kinetic studies on the allosteric transition of phosphoglycerate dehydrogenase." J Biol Chem 1977;252(5);1527-38. PMID: 320209

Hindson03: Hindson VJ, Shaw WV (2003). "Random-order ternary complex reaction mechanism of serine acetyltransferase from Escherichia coli." Biochemistry 42(10);3113-9. PMID: 12627979

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Nagy95: Nagy PL, Marolewski A, Benkovic SJ, Zalkin H (1995). "Formyltetrahydrofolate hydrolase, a regulatory enzyme that functions to balance pools of tetrahydrofolate and one-carbon tetrahydrofolate adducts in Escherichia coli." J Bacteriol 1995;177(5);1292-8. PMID: 7868604

Sugimoto68a: Sugimoto E, Pizer LI (1968). "The mechanism of end product inhibition of serine biosynthesis. II. Optical studies of phosphoglycerate dehydrogenase." J Biol Chem 1968;243(9);2090-8. PMID: 4296829

Woolfolk67: Woolfolk CA, Stadtman ER (1967). "Regulation of glutamine synthetase. 3. Cumulative feedback inhibition of glutamine synthetase from Escherichia coli." Arch Biochem Biophys 118(3);736-55. PMID: 4860415

Zhao96: Zhao G, Winkler ME (1996). "A novel alpha-ketoglutarate reductase activity of the serA-encoded 3-phosphoglycerate dehydrogenase of Escherichia coli K-12 and its possible implications for human 2-hydroxyglutaric aciduria." J Bacteriol 1996;178(1);232-9. PMID: 8550422


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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Thu Nov 27, 2014, biocyc13.