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discounted EARLY registration ends Dec 31, 2014
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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for maintenance.
Metabolic Modeling Tutorial
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BioCyc websites down
12/28 - 12/31
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Metabolic Modeling Tutorial
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BioCyc websites down
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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
glycine + 5,10-methylene-tetrahydromethanopterin + H2O = L-serine + tetrahydromethanopterin
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 Sat Dec 20, 2014, BIOCYC14A.