Escherichia coli K-12 substr. MG1655 Compound: D-serine

Superclasses: an acid all carboxy acids a carboxylate an amino acid a D-amino acid
an acid all carboxy acids a carboxylate an amino acid serine
an amino acid or its derivative an amino acid a D-amino acid
an amino acid or its derivative an amino acid serine

Component of: DsdC-D-serine DNA binding transcriptional dual regulator (summary available)

Chemical Formula: C3H7NO3

Molecular Weight: 105.09 Daltons

Monoisotopic Molecular Weight: 105.0425930962 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


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

Standard Gibbs Free Energy of Change Formation (ΔfG in kcal/mol): -124.15

Reactions known to consume the compound:

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

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

Reactions known to produce the compound:

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

Not in pathways:
a carboxylic ester + H2O → an alcohol + a carboxylate + H+
an aldehyde + NADP+ + H2O → a carboxylate + NADPH + 2 H+
an acyl phosphate + H2O → a carboxylate + phosphate + H+
an acyl-CoA + H2O → a carboxylate + coenzyme A + H+
a 1-acyl 2-lyso-phosphatidylcholine + H2O → a carboxylate + sn-glycero-3-phosphocholine + H+

In Reactions of unknown directionality:

Not in pathways:
DsdC + D-serine = DsdC DNA-binding transcriptional dual regulator
D-serine = pyruvate + ammonium

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

Not in pathways:
a 2-acyl 1-lyso-phosphatidylcholine + H2O = a carboxylate + sn-glycero-3-phosphocholine + H+
an aldehyde[periplasmic space] + FAD[periplasmic space] + H2O[periplasmic space] = a carboxylate[periplasmic space] + FADH2[periplasmic space]

In Transport reactions:
D-serine[periplasmic space] + H+[periplasmic space]D-serine[cytosol] + H+[cytosol] ,
D-serine[periplasmic space]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 [Newman80a, Cicchillo04]

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

In Growth Media: PMA nitrogen source test + D-serine , PMA carbon source test + D-serine

Transcription Units regulated by related protein DsdC-D-serine DNA binding transcriptional dual regulator (3 total):

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


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.

Newman80a: 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

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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