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

Escherichia coli K-12 substr. MG1655 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): -122.1

Reactions known to consume the compound:

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

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

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

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

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

tryptophan biosynthesis :
indole + L-serine → 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

Reactions known to produce the compound:

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

Not in pathways:
glycerophosphoserine + H2O → sn-glycerol 3-phosphate + L-serine + 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
amino acids(n) + H2O → a standard α amino acid + amino acids(n-1)
β-aspartyl dipeptide + H2O → L-aspartate + a standard α amino acid
a dipetide with L-aspartate at the N-terminal + 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


a polypeptide + H2O → a polypeptide + an L-amino acid

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

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

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

In Reactions of unknown directionality:

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


L-methionine + a 2-oxo carboxylate = 2-oxo-4-methylthiobutanoate + a standard α amino acid


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

In Transport reactions:
Na+[periplasmic space] + L-serine[periplasmic space] → Na+[cytosol] + L-serine[cytosol] ,
L-serine[periplasmic space] + H+[periplasmic space]L-serine[cytosol] + H+[cytosol] ,
an L-amino acid[cytosol]an L-amino acid[periplasmic 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: α-ketoglutarate reductase [Zhao96] , D-3-phosphoglycerate dehydrogenase [Winicov75]

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

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


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Sat Dec 20, 2014, BIOCYC13B.