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Escherichia coli K-12 substr. MG1655 Compound: glycine

Abbrev Name: gly

Synonyms: G, aminoacetic acid, gly

Superclasses: an acidall carboxy acidsa carboxylatean amino acida neutral amino acid
an acidall carboxy acidsa carboxylatean amino acida non-polar amino acid
an acidall carboxy acidsa carboxylatean amino acida polar amino acidan uncharged polar amino acid
an acidall carboxy acidsa carboxylatean amino acidan alpha amino acida standard alpha amino acid
an amino acid or its derivativean amino acida neutral amino acid
an amino acid or its derivativean amino acida non-polar amino acid
an amino acid or its derivativean amino acida polar amino acidan uncharged polar amino acid
an amino acid or its derivativean amino acidan alpha amino acida standard alpha amino acid


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

Chemical Formula: C2H5NO2

Molecular Weight: 75.067 Daltons

Monoisotopic Molecular Weight: 76.039853442 Daltons

glycine compound structure

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 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

peptidoglycan maturation (meso-diaminopimelate containing) :
a nascent peptidoglycan with (L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanine) tetrapeptide[periplasm] + glycine[periplasm] → a nascent peptidoglycan with (L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-glycine) tetrapeptide[periplasm] + D-alanine[periplasm]

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

Reactions known to produce the compound:

L-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

Not in pathways:
a peptide with an N-terminal X-L-proline + H2O → a standard α amino acid + a peptide with an N-terminal L-proline + H+
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
β-aspartyl dipeptide + H2O → L-aspartate + a standard α amino acid
a dipetide with an N-terminal L-aspartate + 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

Not in pathways:
a carboxylic ester + H2O → an alcohol + a carboxylate + H+
an aldehyde + NADP+ + H2O → a carboxylate + NADPH + 2 H+
an acyl phosphate + H2O → a carboxylate + phosphate + H+
an acyl-CoA + H2O → a carboxylate + coenzyme A + H+
a 1-acyl 2-lyso-phosphatidylcholine + H2O → a carboxylate + sn-glycero-3-phosphocholine + H+

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

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

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 uridine34 in tRNA + GTP + a 5,10-methylene-tetrahydrofolate + glycine + an oxidized unknown electron acceptor + H2O = a 5-carboxymethylaminomethyluridine in tRNA + GDP + a 7,8-dihydrofolate + an reduced unknown electron acceptor + phosphate + 2 H+
a 2-thiouridine34 in tRNA + GTP + glycine + a 5,10-methylene-tetrahydrofolate + H2O = a 5-carboxymethylaminomethyl-2-thiouridine in tRNA + GDP + a 7,8-dihydrofolate + phosphate
GcvA + glycine = GcvA-gly
GcvR + glycine = GcvR-gly

Not in pathways:
L-methionine + a 2-oxo carboxylate = 2-oxo-4-methylthiobutanoate + a standard α amino acid

Not in pathways:
a 5-L-glutamyl-[peptide][periplasm] + an amino acid[periplasm] = a 5-L-glutamyl-amino acid[periplasm] + a peptide[periplasm]

Not in pathways:
a 2-acyl 1-lyso-phosphatidylcholine + H2O = a carboxylate + sn-glycero-3-phosphocholine + H+
an aldehyde[periplasm] + FAD[periplasm] + H2O[periplasm] = a carboxylate[periplasm] + FADH2[periplasm]

In Transport reactions:
glycine[periplasm] + H+[periplasm]glycine[cytosol] + H+[cytosol],
glycine[periplasm]glycine[cytosol],
an amino acid[periplasm]an amino acid[extracellular space]

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

Inhibitor (Competitive) of: serine acetyltransferase [Hindson03] Inhibitor (Allosteric) of: (S)-2-hydroxyglutarate reductase [Zhao96], (R)-2-hydroxyglutarate reductase [Zhao96], D-3-phosphoglycerate dehydrogenase [Zhao96, Dubrow77, Sugimoto68a] Inhibitor (Mechanism unknown) of: glutamine synthetase [Woolfolk67, Comment 1], formyltetrahydrofolate deformylase [Nagy95]

This compound has been characterized as an alternative substrate of the following enzymes: L,D-transpeptidase, D-alanine-D-alanine ligase B, L,D-transpeptidase, D-alanine-D-alanine ligase A, L,D-transpeptidase, UDP-N-acetylmuramate-alanine ligase

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
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