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discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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MetaCyc Compound: L-serine

Abbrev Name: ser

Synonyms: S, serine, ser, L-ser

Superclasses: an amino acid or its derivative an amino acid a neutral 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
an amino acid or its derivative an amino acid an L-amino acid
an amino acid or its derivative an amino acid serine

Chemical Formula: C3H7NO3

Molecular Weight: 105.09 Daltons

Monoisotopic Molecular Weight: 105.0425930962 Daltons

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 Change Formation (ΔfG in kcal/mol): -50.20216 Inferred 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+
CDP-2,3-bis-O-(geranylgeranyl)-sn-glycerol + 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 :
L-serine + H+ → ethanolamine + CO2

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

enterobactin biosynthesis :
3 L-serine + 3 2,3-dihydroxybenzoate + 6 ATP → enterobactin + 6 AMP + 6 diphosphate + 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

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 + [PigH PKS] + 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 + 2 H+ + 12 H2O

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

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

tRNA charging :
tRNAser + L-serine + ATP + H+ → L-seryl-tRNAser + AMP + diphosphate

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

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

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

prodigiosin biosynthesis :
(S)-3-acetyloctanal + an L-amino acid → 2-methyl-3-n-amyl-dihydropyrrole + a 2-oxo acid + H2O

rhizocticin A and B biosynthesis :
2-keto-5-phosphono-3-cis-pentenoate + an L-amino acidL-2-amino-5-phosphono-3-cis-pentenoate + a 2-oxo carboxylate
2-keto-4-hydroxy-5-phosphonopentanoate + an L-amino acid → 2-amino-4-hydroxy-5-phosphonopentanoate + a 2-oxo carboxylate


ATP + 2 an L-amino acid → ADP + a dipeptide + phosphate + H+

Reactions known to produce the compound:

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

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

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)


L(or D)-O-phosphoserine + H2O + H+serine + phosphate

γ-glutamyl cycle :
an (γ-L-glutamyl)-L-amino acid → an L-amino acid + 5-oxoproline


a peptide + H2O → an L-amino acid + a peptide
a peptide + H2O → a peptide + an L-amino acid
a N-methyl L-amino acid + oxygen + H2O → an L-amino acid + formaldehyde + hydrogen peroxide
a polypeptide + H2O → a polypeptide + an L-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:

cysteine biosynthesis/homocysteine degradation , homocysteine and cysteine interconversion :
L-homocysteine + L-serine ↔ L-cystathionine + H2O

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

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

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

phospholipid biosynthesis II :
an L-1-phosphatidyl-ethanolamine + L-serine ↔ an L-1-phosphatidylserine + ethanolamine
a CDP-diacylglycerol + L-serine ↔ CMP + an L-1-phosphatidylserine + H+

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

Not in pathways:
L-serine + ATP ↔ L-seryl-AMP + diphosphate
pyruvate + L-serine ↔ L-alanine + hydroxypyruvate

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


L-alanine + a 2-oxo carboxylate ↔ pyruvate + an L-amino acid

In Reactions of unknown directionality:

Not in pathways:
5,10-methylene-tetrahydromethanopterin + glycine + H2O = tetrahydromethanopterin + L-serine
(S)-2-amino-3-(3-hydroxy-4-oxo-4h-pyridin-1-yl)propanoate + H+ + H2O = L-serine + 3-hydroxy-4h-pyrid-4-one
'activated' tRNA + L-cysteine = L-serine + tRNA containing a thionucleotide
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 + NADP+ = 2-aminomalonate-semialdehyde + NADPH + 2 H+
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+


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


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

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

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: α-ketoglutarate reductase [Zhao96] , D-3-phosphoglycerate dehydrogenase [Winicov75]

Inhibitor (Mechanism unknown) of: phosphoserine phosphatase [Pizer63, Comment 1] , glutamine synthetase [Comment 2] , serine acetyltransferase [Kredich66] , phosphoserine phosphatase [Knox69] , 3-phosphoserine phosphatase [Ho99]


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
Page generated by SRI International Pathway Tools version 18.5 on Sun Nov 23, 2014, biocyc14.