Metabolic Modeling Tutorial
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites MAYBE down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites MAYBE down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites MAYBE down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites MAYBE down
12/28 - 12/31
for maintenance.
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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 [Hirata65]

Inhibitor (Mechanism unknown) of: L-serine deaminase [Newman80a, 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

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."

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


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 Fri Dec 26, 2014, BIOCYC13A.