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Escherichia coli K-12 substr. MG1655 Compound: L-serine

Abbrev Name: ser

Synonyms: S, serine, ser, L-ser

Superclasses: an acidall carboxy acidsa carboxylatean amino acida neutral 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 acidall carboxy acidsa carboxylatean amino acidan L-amino acid
an acidall carboxy acidsa carboxylatean amino acidserine
an amino acid or its derivativean amino acida neutral 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
an amino acid or its derivativean amino acidan L-amino acid
an amino acid or its derivativean amino acidserine


Chemical Formula: C3H7NO3

Molecular Weight: 105.09 Daltons

Monoisotopic Molecular Weight: 106.0504181283 Daltons

L-serine compound structure

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

InChI: InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m0/s1

InChIKey: InChIKey=MTCFGRXMJLQNBG-REOHCLBHSA-N

Unification Links: CAS:56-45-1, ChEBI:33384, HMDB:HMDB00187, IAF1260:33717, KEGG:C00065, MetaboLights:MTBLC33384, PubChem:6857581

Standard Gibbs Free Energy of Formation (ΔfG in kcal/mol): -122.1

Reactions known to consume the compound:

L-cysteine biosynthesis I :
L-serine + acetyl-CoA → O-acetyl-L-serine + coenzyme A

L-selenocysteine biosynthesis I (bacteria) :
a tRNAsec + L-serine + ATP + H+ → an L-seryl-[tRNAsec] + AMP + diphosphate

L-serine degradation :
L-serine → 2-aminoprop-2-enoate + H+ + H2O

L-tryptophan biosynthesis :
indole + L-serine → L-tryptophan + H2O

tRNA charging :
a tRNAser + L-serine + ATP + H+ → an L-seryl-[tRNAser] + AMP + diphosphate

Not in pathways:
L-serine → pyruvate + ammonium
6 ATP + 3 L-serine + 3 2,3-dihydroxybenzoate → 6 AMP + enterobactin + 6 diphosphate + 3 H+
(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine → L-tryptophan + D-glyceraldehyde 3-phosphate + H2O

Reactions known to produce the compound:

L-serine biosynthesis :
3-phospho-L-serine + H2O → L-serine + phosphate

Not in pathways:
glycerophosphoserine + H2O → sn-glycerol 3-phosphate + L-serine + H+

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 polypeptide + H2O → a polypeptide + an L-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:

enterobactin biosynthesis :
L-serine + ATP + H+ ↔ L-seryl-adenylate + diphosphate

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

phosphatidylethanolamine biosynthesis I :
a CDP-diacylglycerol + L-serine ↔ CMP + an L-1-phosphatidylserine + H+

In Reactions of unknown directionality:

Not in pathways:
'activated' tRNA + L-cysteine = L-serine + tRNA containing a thionucleotide
L-serine + NADP+ = 2-aminoacetaldehyde + CO2 + NADPH
L-serine + NADP+ = 2-aminomalonate semialdehyde + NADPH + H+

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:
Na+[periplasm] + L-serine[periplasm] → Na+[cytosol] + L-serine[cytosol],
L-serine[periplasm] + H+[periplasm]L-serine[cytosol] + H+[cytosol],
an amino acid[periplasm]an amino acid[extracellular space]

Enzymes inhibited by L-serine, sorted by the type of inhibition, are:

Inhibitor (Competitive) of: D-serine ammonia-lyase [Labow66, Schnackerz99] Inhibitor (Allosteric) of: (S)-2-hydroxyglutarate reductase [Zhao96], (R)-2-hydroxyglutarate reductase [Zhao96], D-3-phosphoglycerate dehydrogenase [Winicov75] Inhibitor (Mechanism unknown) of: glutamine synthetase [Comment 1], phosphoserine phosphatase [Pizer63, Comment 2], serine acetyltransferase [Kredich66]

This compound has been characterized as an alternative substrate of the following enzymes: 8-amino-7-oxononanoate synthase, phenylserine aldolase, UDP-N-acetylmuramate-alanine ligase, alanine racemase

In Growth Media: PMA carbon source test + ser, Neidhardt EZ rich defined medium, PMA nitrogen source test + ser


References

Kredich66: Kredich NM, Tomkins GM (1966). "The enzymic synthesis of L-cysteine in Escherichia coli and Salmonella typhimurium." J Biol Chem 1966;241(21);4955-65. PMID: 5332668

Labow66: Labow R, Robinson WG (1966). "Crystalline D-serine dehydrase." J Biol Chem 1966;241(5);1239-43. PMID: 5327101

Pizer63: Pizer LI (1963). "The pathway and control of serine biosynthesis in Escherichia coli." J Biol Chem 1963;238:3934-3944. PMID: 14086727

Schnackerz99: Schnackerz KD, Tai CH, Potsch RK, Cook PF (1999). "Substitution of pyridoxal 5'-phosphate in D-serine dehydratase from Escherichia coli by cofactor analogues provides information on cofactor binding and catalysis." J Biol Chem 274(52);36935-43. PMID: 10601247

Umbarger63: Umbarger HE, Umbarger MA, Siu PML (1963). "Biosynthesis of serine in Escherichia coli and Salmonella typhimurium." J Bacteriol 85:1431-1439. PMID: 14047241

Winicov75: Winicov I (1975). "The mechanism of end product inhibition of serine biosynthesis. V. Mechanism of serim inhibition of phosphoglycerate dehydrogenases." J Biol Chem 250(5);1640-7. PMID: 234462

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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