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MetaCyc 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): -50.20216Inferred by computational analysis [Latendresse13]

Reactions known to consume the compound:

achromobactin biosynthesis :
citrate + ATP + L-serineO-citryl-L-serine + AMP + diphosphate

archaetidylserine and archaetidylethanolamine biosynthesis :
saturated CDP-archaeol + L-serine → saturated archaetidylserine + CMP + H+
unsaturated CDP-archaeol + L-serine → unsaturated archaetidylserine + CMP + H+

ceramide de novo biosynthesis , sphingolipid biosynthesis (plants) , sphingolipid biosynthesis (yeast) :
L-serine + palmitoyl-CoA + H+ → CO2 + 3-dehydrosphinganine + coenzyme A

choline biosynthesis I , phosphatidylethanolamine biosynthesis II :
L-serine + H+ → ethanolamine + CO2

D-cycloserine biosynthesis , L-cysteine biosynthesis I , seleno-amino acid biosynthesis :
L-serine + acetyl-CoA → O-acetyl-L-serine + coenzyme A

D-serine metabolism , vancomycin resistance II :
L-serine → D-serine

dapdiamides biosynthesis :
L-serine + ammonium → (S)-2,3-diaminopropanoate + H2O

echinomycin and triostin A biosynthesis :
quinoxaline-2-carboxyl-[acyl-carrier protein] + L-serine + L-alanine + non-ribosomal peptide synthase + 2 ATP → quinoxaline-2-carboxyl-D-seryl-L-alanyl-[non-ribosomal peptide synthase] + a holo-[acyl-carrier protein] + 2 ADP + 2 phosphate + 2 H+

equisetin biosynthesis :
1-[(1S,2R,4aS,6R,8aR)-1,6-dimethyl-2-[(1E)-prop-1-en-1-yl)]-1,2,4a,5,6,7,8,8a-octahydronaphthalen-1-yl]butane-1,3-dioyl-[acp] + L-serine + ATP → trichosetin + a holo-[acyl-carrier protein] + AMP + diphosphate + H+

ferrichrome A biosynthesis :
3 methylglutaconyl hydroxy ornithine + 3 ATP + glycine + 2 L-serine + Fe3+ → ferrichrome A + 3 AMP + 3 diphosphate + 3 H2O + 3 H+

gliotoxin biosynthesis :
L-phenylalanine + L-serine + 2 ATP → cyclo(L-Phe-L-Ser) + 2 ADP + 2 phosphate + 2 H+

glycine betaine degradation I , L-serine degradation , purine nucleobases degradation II (anaerobic) :
L-serine → 2-aminoprop-2-enoate + H+ + H2O

guadinomine B biosynthesis :
a holo-[seryl-carrier protein] + L-serine + ATP → an L-seryl-[seryl-carrier protein] + AMP + diphosphate

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

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

lathyrine biosynthesis :
2-amino-4-carboxypyrimidine + L-serine + H+ → lathyrine + CO2 + H2O

phosphatidylserine biosynthesis I :
a phosphatidylcholine + L-serine → an L-1-phosphatidylserine + choline

prodigiosin biosynthesis :
3-oxo-3-(1H-pyrrol-2-yl)propanoyl-S-[PigH] + L-serine → 4-hydroxy-2,2'-bipyrrole-5-methanol + a holo-[PigH polyketide synthase/peptidyl-carrier protein] + CO2 + H2O

pyoverdine I biosynthesis :
L-glutamate + L-tyrosine + L-2,4-diaminobutanoate + 2 L-serine + L-arginine + 2 N5-formyl-N5-hydroxy-L-ornithine + L-lysine + 2 L-threonine → ferribactin + 12 H2O + H+

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

zwittermicin A biosynthesis :
a fatty acid + L-asparagine + L-serine + malonyl-CoA + an aminomalonyl-[seryl-carrier protein] + a (2R)-2-hydroxymalonyl-[acp] + β-ureidoalanine + L-alanine + polyketide synthase + 8 NADPH + oxygen + 12 H+ → proto-zwittermicin A-L-alaninyl-[PKS] + 2 CO2 + a holo-[seryl-carrier protein] + a holo-[acyl-carrier protein] + coenzyme A + 8 NADP+ + 9 H2O
L-serine + ammonium → (S)-2,3-diaminopropanoate + H2O
a holo-[seryl-carrier protein] + L-serine + ATP → an L-seryl-[seryl-carrier protein] + AMP + diphosphate

Not in pathways:
3 L-serine + 3 2,3-dihydroxybenzoate + 6 ATP → enterobactin + 6 AMP + 6 diphosphate + 3 H+

Reactions known to produce the compound:

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

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

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

Not in pathways:
amino acids(n) + H2O → a standard α amino acid + amino acids(n-1)
amino acids(n) + H2O → amino acids(n-1) + a standard α amino acid
amino acids(n) + H2O → amino acids(n-1) + a standard α amino acid
a dipetide with L-histidine at the C-terminal + H2O → a standard α amino acid + L-histidine
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 dipeptide + H2O → 2 amino acids
β-aspartyl dipeptide + H2O → L-aspartate + 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 an N-terminal L-aspartate + H2O → L-aspartate + a standard α amino acid

Reactions known to both consume and produce the compound:

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

folate polyglutamylation , folate transformations I , folate transformations II , glycine betaine degradation I , glycine betaine degradation II (mammalian) , glycine biosynthesis I , N10-formyl-tetrahydrofolate biosynthesis , purine nucleobases degradation II (anaerobic) :
L-serine + a tetrahydrofolate ↔ glycine + a 5,10-methylene-tetrahydrofolate + H2O

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

L-cysteine biosynthesis III (from L-homocysteine) , L-homocysteine and L-cysteine interconversion :
L-homocysteine + L-serine ↔ L-cystathionine + H2O

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

phosphatidylethanolamine biosynthesis III , phosphatidylserine biosynthesis II :
an L-1-phosphatidylethanolamine + L-serine ↔ an L-1-phosphatidylserine + ethanolamine

photorespiration :
L-serine + a tetrahydrofolate ↔ glycine + a 5,10-methylene-tetrahydrofolate + H2O
glyoxylate + L-serine ↔ hydroxypyruvate + glycine

superpathway of phospholipid biosynthesis II (plants) :
an L-1-phosphatidylethanolamine + L-serine ↔ an L-1-phosphatidylserine + ethanolamine
a CDP-diacylglycerol + L-serine ↔ CMP + an L-1-phosphatidylserine + H+

Not in pathways:
pyruvate + L-serine ↔ L-alanine + hydroxypyruvate

dimethylsulfoniopropanoate 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

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

L-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

Not in pathways:
L-ornithine + a 2-oxo carboxylate ↔ a standard α amino acid + L-glutamate-5-semialdehyde

Not in pathways:
L-alanine + a 2-oxo carboxylate ↔ pyruvate + an L-amino acid

sphingolipid recycling and degradation (yeast) :
a dihydroceramide + H2O ↔ D-erythro-sphinganine + a carboxylate

In Reactions of unknown directionality:

Not in pathways:
5,10-methylene-tetrahydromethanopterin + glycine + H2O = tetrahydromethanopterin + L-serine
L-mimosine + H+ + H2O = L-serine + 3-hydroxy-4h-pyrid-4-one
'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+
L-serine + NAD+ = 2-aminoacetaldehyde + CO2 + NADH
L-serine + NAD+ = 2-aminomalonate semialdehyde + NADH + H+
4-O-dimethylallyl-L-tyrosine + L-serine = phomamide + 2 H2O
L-serine + NAD+ + H2O = ammonium + hydroxypyruvate + NADH + H+
pyrazole + L-serine = 3-(pyrazol-1-yl)-L-alanine + H2O
L-serine + 2-oxoglutarate = L-glutamate + hydroxypyruvate
L-serine + diphosphate = 3-phospho-L-serine + phosphate + H+
L-serine + CDP-ethanolamine = L-serine-phosphoethanolamine + CMP + H+

Not in pathways:
L-arginine + a standard α amino acid + ATP = a dipeptide with N-terminal L-arginine + ADP + phosphate + H+

Not in pathways:
an L-amino acid = a D-amino acid
an L-amino acid + NAD+ + H2O = a 2-oxo carboxylate + ammonium + NADH + H+
an N-carbamoyl-L-amino acid + H2O + 2 H+ = an L-amino acid + ammonium + CO2
S-ureidoglycine + a 2-oxo carboxylate = oxalurate + an L-amino acid

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

Not in pathways:
eugenol + a carboxylate + NADP+ = a coniferyl ester + NADPH
a 2-acyl 1-lyso-phosphatidylcholine[periplasm] + H2O[periplasm] = a carboxylate[periplasm] + sn-glycero-3-phosphocholine[periplasm] + H+[periplasm]
an aldehyde + an electron-transfer quinone + H2O = a carboxylate + an electron-transfer quinol + H+
a triacyl-sn-glycerol + H2O = a 1,2-diacyl-sn-glycerol + a carboxylate + H+
a penicillin + H2O = 6-aminopenicillanate + a carboxylate
an aldehyde[periplasm] + FAD[periplasm] + H2O[periplasm] = a carboxylate[periplasm] + FADH2[periplasm]

In Transport reactions:
2 L-serine[out] + 2 H+[out] ↔ 2 L-serine[in] + 2 H+[in],
L-serine[periplasm] + H+[periplasm]L-serine[cytosol] + H+[cytosol],
Na+[periplasm] + L-serine[periplasm] → Na+[cytosol] + L-serine[cytosol],
a polar amino acid[extracellular space] + ATP + H2O ↔ a polar amino acid[cytosol] + ADP + phosphate

Enzymes activated by L-serine, sorted by the type of activation, are:

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

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

Inhibitor (Competitive) of: D-serine ammonia-lyase [Labow66, Schnackerz99], asparagine aminotransferase [Ireland83] Inhibitor (Allosteric) of: (R)-2-hydroxyglutarate reductase [Zhao96], D-3-phosphoglycerate dehydrogenase [Winicov75], (S)-2-hydroxyglutarate reductase [Zhao96] Inhibitor (Mechanism unknown) of: glutamine synthetase [Comment 1], phosphoserine phosphatase [Pizer63, Comment 2], serine acetyltransferase [Kredich66], phosphoserine phosphatase [Knox69], 3-phosphoserine phosphatase [Ho99]

This compound has been characterized as an alternative substrate of the following enzymes: alanine racemase, ornithine racemase, alanopine synthase, phenylserine aldolase, L-alanine dehydrogenase, alanine dehydrogenase, jasmonyl-isoleucine synthetase, N-(4-hydroxybenzoyl)-L-glutamate synthetase, alanopine synthase, UDP-N-acetylmuramate-alanine ligase, 3-hydroxyisobutyrate dehydrogenase, tryptophanase, 3-hydroxypropanonate dehydrogenase, 8-amino-7-oxononanoate synthase, strombine synthase


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

Ho99: Ho CL, Noji M, Saito K (1999). "Plastidic pathway of serine biosynthesis. Molecular cloning and expression of 3-phosphoserine phosphatase from Arabidopsis thaliana." J Biol Chem 274(16);11007-12. PMID: 10196182

Ireland83: Ireland RJ, Joy KW (1983). "Purification and properties of an asparagine aminotransferase from Pisum sativum leaves." Arch Biochem Biophys 223(1);291-6. PMID: 6407397

Knox69: Knox WE, Herzfeld A, Hudson J (1969). "Phosphoserine phosphatase distribution in normal and neoplastic rat tissues." Arch Biochem Biophys 132(2);397-403. PMID: 4307821

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

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

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 PM (1963). "Biosynthesis of serine in Escherichia coli and Salmonella typhimurium." J Bacteriol 85;1431-9. 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 MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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