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discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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Escherichia coli K-12 substr. MG1655 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

Component of:
GcvA-gly
GcvR-gly (summary available)

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): -88.6

Reactions known to consume the compound:

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

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

N10-formyl-tetrahydrofolate biosynthesis :
glycine + a tetrahydrofolate + NAD+ → a 5,10-methylene-tetrahydrofolate + ammonium + CO2 + NADH

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

Reactions known to produce the compound:

threonine degradation IV :
L-threonine → acetaldehyde + glycine

Not in pathways:
L-cysteinyl-glycine + H2O → L-cysteine + glycine
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 peptide + H2O → a standard α amino acid + a peptide
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
amino acids(n) + H2O → a standard α amino acid + amino acids(n-1)
β-aspartyl dipeptide + H2O → L-aspartate + a standard α amino acid
a dipetide with L-aspartate at the N-terminal + H2O → L-aspartate + a standard α amino acid
a tripeptide + H2O → a dipeptide + a standard α amino acid
a dipeptide with proline at the C-terminal + H2O → L-proline + a standard α amino acid
a dipeptide + H2O → 2 a standard α amino acid

Reactions known to both consume and produce the compound:

folate polyglutamylation , glycine biosynthesis I , N10-formyl-tetrahydrofolate biosynthesis :
L-serine + a tetrahydrofolate ↔ glycine + a 5,10-methylene-tetrahydrofolate + H2O

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

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

Not in pathways:
L-allo-threonine ↔ glycine + acetaldehyde
DL-allothreonine ↔ acetaldehyde + glycine
4-hydroxy-L-threonine ↔ glycolaldehyde + glycine

In Reactions of unknown directionality:

Not in pathways:
L-threo-3-phenylserine = benzaldehyde + glycine
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
a tRNA uridine34 + GTP + a 5,10-methylene-tetrahydrofolate + glycine + H2O = a tRNA containing 5-carboxymethylaminomethyluridine + GDP + a 7,8-dihydrofolate + phosphate
GcvA + glycine = GcvA-gly
GcvR + glycine = GcvR-gly


L-methionine + a 2-oxo carboxylate = 2-oxo-4-methylthiobutanoate + a standard α amino acid


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

In Transport reactions:
glycine[periplasmic space] + H+[periplasmic space]glycine[cytosol] + H+[cytosol] ,
glycine[periplasmic space]glycine[cytosol]

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]

In Growth Media: Neidhardt EZ rich defined medium , Gutnick minimal salts medium base + gly , PMA nitrogen source test + gly , PMA carbon source test + gly


References

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

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 EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Sun Nov 23, 2014, biocyc13.