Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
twitter

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


Report Errors or Provide Feedback
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 Dec 21, 2014, BIOCYC13B.