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
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

MetaCyc Compound: D-serine

Superclasses: an amino acid or its derivative an amino acid a D-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-/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 Change Formation (ΔfG in kcal/mol): -52.25216 Inferred 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-related quinone[CCO-OUT-CCO-IN] + H2O[in] → a 2-oxo carboxylate[in] + ammonium[in] + an electron-transfer-related quinol[CCO-OUT-CCO-IN]
a D-amino acid + oxygen + H2O → ammonium + hydrogen peroxide + a 2-oxo carboxylate

Reactions known to produce the compound:

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

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


a D-aminoacyl-tRNA + H2O → a D-amino acid + a tRNA + 2 H+
a protein with N-terminal D-amino acid + H2O → a peptide + a D-amino acid

In Reactions of unknown directionality:

Not in pathways:
D-serine = pyruvate + ammonium


acetyl-CoA + a D-amino acid = an N-acetyl-D-amino acid + coenzyme A + H+
an N-carbamoyl D-amino acid + H+ + H2O = 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


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

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-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 [Hirata65a]

Inhibitor (Mechanism unknown) of: L-serine deaminase [Newman80b, Cicchillo04]


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

Hirata65a: 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."

Newman80b: 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
Page generated by SRI International Pathway Tools version 18.5 on Tue Nov 25, 2014, BIOCYC14B.