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MetaCyc Compound: D-serine

Superclasses: an acidall carboxy acidsa carboxylatean amino acida D-amino acid
an acidall carboxy acidsa carboxylatean amino acidserine
an amino acid or its derivativean amino acida D-amino acid
an amino acid or its derivativean amino acidserine

Chemical Formula: C3H7NO3

Molecular Weight: 105.09 Daltons

Monoisotopic Molecular Weight: 106.0504181283 Daltons

D-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-/m1/s1

InChIKey: InChIKey=MTCFGRXMJLQNBG-UWTATZPHSA-N

Unification Links: CAS:312-84-5, ChEBI:35247, HMDB:HMDB03406, IAF1260:35846, KEGG:C00740, MetaboLights:MTBLC35247, PubChem:6857549

Standard Gibbs Free Energy of Formation (ΔfG in kcal/mol): -52.25216Inferred by computational analysis [Latendresse13]

Reactions known to consume the compound:

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

vancomycin resistance II :
D-alanine + D-serine + ATP → D-alanyl-D-serine + ADP + phosphate + H+

Not in pathways:
a D-amino acid[in] + an electron-transfer quinone[membrane] + H2O[in] → a 2-oxo carboxylate[in] + ammonium[in] + an electron-transfer quinol[membrane]
a D-amino acid + oxygen + H2O → ammonium + hydrogen peroxide + a 2-oxo carboxylate

3-hydroxy-L-homotyrosine biosynthesis :
4-(4-hydroxyphenyl)-2-oxobutanoate + an amino acidL-homotyrosine + a 2-oxo acid

methyl ketone biosynthesis :
a carboxylate + ATP + coenzyme A → an acyl-CoA + AMP + diphosphate

Not in pathways:
a carboxylate + GTP + coenzyme A → an acyl-CoA + GDP + phosphate

Reactions known to produce the compound:

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

Not in pathways:
L(or D)-O-phosphoserine + H2O + H+serine + phosphate

Not in pathways:
a peptide with an N-terminal D-amino acid + H2O → a peptide + a D-amino acid + H+
a D-aminoacyl-[tRNA] + H2O → a D-amino acid + an uncharged tRNA + 2 H+

3,3'-thiodipropanoate degradation :
3-sulfinopropionate + an acyl-CoA → 3-sulfinopropanoyl-CoA + a carboxylate

dimethylsulfoniopropanoate degradation II (cleavage) :
dimethylsulfoniopropanoate + an acyl-CoA → dimethylsulfoniopropioyl-CoA + a carboxylate

NAD/NADP-NADH/NADPH mitochondrial interconversion (yeast) :
an aldehyde + NADP+ + H2O → a carboxylate + NADPH + 2 H+
an aldehyde + NAD+ + H2O → a carboxylate + NADH + 2 H+

phosphatidylcholine resynthesis via glycerophosphocholine :
a phosphatidylcholine + 2 H2O → sn-glycero-3-phosphocholine + 2 a carboxylate + 2 H+

Not in pathways:
a 1-acyl 2-lyso-phosphatidylcholine[periplasm] + H2O[periplasm]a carboxylate[periplasm] + sn-glycero-3-phosphocholine[periplasm] + H+[periplasm]
an acyl-CoA + H2O → a carboxylate + coenzyme A + H+
an L-1-phosphatidyl-inositol + H2O → a 1-acyl-sn-glycero-3-phospho-D-myo-inositol + a carboxylate + H+
a carboxylic ester + H2O → an alcohol + a carboxylate + H+
an aldehyde + oxygen + H2O → a carboxylate + hydrogen peroxide + H+
an acylcholine + H2O → choline + a carboxylate + H+
a 1,2-diacyl-3-O-(β-D-galactopyranosyl)-sn-glycerol + 2 H2O → 2 a carboxylate + 3-β-D-galactosyl-sn-glycerol + 2 H+
an acyl phosphate + H2O → a carboxylate + phosphate + H+
an S-acylglutathione + H2O → a carboxylate + glutathione
an N-acyl-L-aspartate + H2O → L-aspartate + a carboxylate

Reactions known to both consume and produce the compound:

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

In Reactions of unknown directionality:

Not in pathways:
D-serine = pyruvate + ammonium

Not in pathways:
acetyl-CoA + a D-amino acid = an N-acetyl-D-amino acid + coenzyme A + H+
an N-carbamoyl D-amino acid + H2O + 2 H+ = a D-amino acid + ammonium + CO2
an N-acylated-D-amino acid + H2O = a D-amino acid + a carboxylate
an L-amino acid = a D-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]
a nitrile + 2 H2O = a carboxylate + ammonium
an aliphatic nitrile + 2 H2O = a carboxylate + ammonium
an N-acyl-L-homoserine lactone + H2O = L-homoserine lactone + a carboxylate
an aldehyde + an oxidized unknown electron acceptor + H2O = a carboxylate + an reduced unknown electron acceptor + H+
an N-acylated aromatic-L-amino acid + H2O = a carboxylate + an aromatic L-amino acid
an N-acylated-D-amino acid + H2O = a D-amino acid + a carboxylate
an N-acylated aliphatic-L-amino acid + H2O = a carboxylate + an aliphatic L-amino acid
a D-hexose + an acyl phosphate = a D-hexose-phosphate + a carboxylate
an aldehyde + 2 an oxidized ferredoxin [iron-sulfur] cluster + H2O = a carboxylate + 2 a reduced ferredoxin [iron-sulfur] cluster + 3 H+
an aldehyde + NAD(P)+ + H2O = a carboxylate + NAD(P)H + 2 H+
an N-acyl-D-glutamate + H2O = a carboxylate + D-glutamate
an anilide + H2O = aniline + a carboxylate + H+
a 5'-acylphosphoadenosine + H2O = a carboxylate + AMP + 2 H+

In Transport reactions:
D-serine[periplasm] + H+[periplasm]D-serine[cytosol] + H+[cytosol],
D-serine[periplasm]D-serine[cytosol]

In Redox half-reactions:
a 2-oxo carboxylate[in] + ammonium[in] + 2 H+[in] + 2 e-[membrane]a D-amino acid[in] + H2O[in]

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

Inhibitor (Competitive) of: aspartate 1-decarboxylase [Cronan80], threonine dehydratase [Hirata65] Inhibitor (Mechanism unknown) of: L-serine deaminase [Newman80, Cicchillo04]

This compound has been characterized as an alternative substrate of the following enzymes: alanine racemase, D-alanine-D-alanine ligase B, L-allo-threonine dehydrogenase, 3-hydroxy acid dehydrogenase, D-threo-3-hydroxyaspartate ammonia-lyase


References

Cicchillo04: Cicchillo RM, Baker MA, Schnitzer EJ, Newman EB, Krebs C, Booker SJ (2004). "Escherichia coli L-serine deaminase requires a [4Fe-4S] cluster in catalysis." J Biol Chem 279(31);32418-25. PMID: 15155761

Cronan80: Cronan JE (1980). "Beta-alanine synthesis in Escherichia coli." J Bacteriol 1980;141(3);1291-7. PMID: 6767707

Hirata65: Hirata M, Tokushige M, Inagaki A, Hayaishi O (1965). "Nucleotide activation of threonine deaminase from Escherichia coli." The Journal of Biological Chemistry 1965; 240:1711-1717. PMID: 14285512

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

Newman80: Newman EB, Kapoor V (1980). "In vitro studies on L-serine deaminase activity of Escherichia coli K12." Can J Biochem 1980;58(11);1292-7. PMID: 7011505


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
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