Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB000497
Identification
Name: D-Serine
Description:Serine is important in metabolism in that it participates in the biosynthesis of purines and pyrimidines. It is the precursor to several amino acids including glycine and cysteine, and tryptophan in bacteria. It is also the precursor to numerous of other metabolites, including sphingolipids and folate, which is the principal donor of one-carbon fragments in biosynthesis. Serine dehydratase is an enzyme that converts serine to pyruvate.
Structure
Thumb
Synonyms:
  • (2R)-2-amino-3-hydroxypropanoate
  • (2R)-2-amino-3-hydroxypropanoic acid
  • (R)-2-amino-3-hydroxypropanoate
  • (R)-2-amino-3-hydroxypropanoic acid
  • D-Ser
  • D-Serin
  • DL-Serine
  • DSN
  • Serine D-form
Chemical Formula: C3H7NO3
Average Molecular Weight: 105.0926
Monoisotopic Molecular Weight: 105.042593095
InChI Key: MTCFGRXMJLQNBG-UWTATZPHSA-N
InChI:InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m1/s1
CAS number: 312-84-5
IUPAC Name:(2R)-2-amino-3-hydroxypropanoic acid
Traditional IUPAC Name: D-serine
SMILES:N[C@H](CO)C(O)=O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom.
Kingdom Organic compounds
Super ClassOrganic acids and derivatives
Class Carboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct Parent D-alpha-amino acids
Alternative Parents
Substituents
  • D-alpha-amino acid
  • Beta-hydroxy acid
  • Hydroxy acid
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Hydrocarbon derivative
  • Primary amine
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Alcohol
  • Aliphatic acyclic compound
Molecular Framework Aliphatic acyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:0
Melting point: 229 °C
Experimental Properties:
PropertyValueSource
Water Solubility:364 mg/mL at 20 oC [BEILSTEIN]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility480.0 mg/mLALOGPS
logP-3.4ALOGPS
logP-3.9ChemAxon
logS0.66ALOGPS
pKa (Strongest Acidic)2.03ChemAxon
pKa (Strongest Basic)8.93ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area83.55 Å2ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity22.04 m3·mol-1ChemAxon
Polarizability9.39 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-MSNot Available
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-03di-9000000000-d33888cff00d0ade0ffeView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-03di-9000000000-f7e50afcb90768dce4a5View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0006-9000000000-043951ed5540cce44f4eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,1H] 2D NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
References
References:
  • Alvarez JV, Greulich H, Sellers WR, Meyerson M, Frank DA: Signal transducer and activator of transcription 3 is required for the oncogenic effects of non-small-cell lung cancer-associated mutations of the epidermal growth factor receptor. Cancer Res. 2006 Mar 15;66(6):3162-8. Pubmed: 16540667
  • Amberger VR, Hensel T, Ogata N, Schwab ME: Spreading and migration of human glioma and rat C6 cells on central nervous system myelin in vitro is correlated with tumor malignancy and involves a metalloproteolytic activity. Cancer Res. 1998 Jan 1;58(1):149-58. Pubmed: 9426071
  • Boehning D, Snyder SH: Novel neural modulators. Annu Rev Neurosci. 2003;26:105-31. Pubmed: 14527267
  • Deshpande RV, Goust JM, Hogan EL, Banik NL: Calpain secreted by activated human lymphoid cells degrades myelin. J Neurosci Res. 1995 Oct 1;42(2):259-65. Pubmed: 8568927
  • Dietze-Schroeder D, Sell H, Uhlig M, Koenen M, Eckel J: Autocrine action of adiponectin on human fat cells prevents the release of insulin resistance-inducing factors. Diabetes. 2005 Jul;54(7):2003-11. Pubmed: 15983200
  • Farhana L, Dawson MI, Huang Y, Zhang Y, Rishi AK, Reddy KB, Freeman RS, Fontana JA: Apoptosis signaling by the novel compound 3-Cl-AHPC involves increased EGFR proteolysis and accompanying decreased phosphatidylinositol 3-kinase and AKT kinase activities. Oncogene. 2004 Mar 11;23(10):1874-84. Pubmed: 14981538
  • Franzke CW, Baici A, Bartels J, Christophers E, Wiedow O: Antileukoprotease inhibits stratum corneum chymotryptic enzyme. Evidence for a regulative function in desquamation. J Biol Chem. 1996 Sep 6;271(36):21886-90. Pubmed: 8702990
  • Hansson L, Stromqvist M, Backman A, Wallbrandt P, Carlstein A, Egelrud T: Cloning, expression, and characterization of stratum corneum chymotryptic enzyme. A skin-specific human serine proteinase. J Biol Chem. 1994 Jul 29;269(30):19420-6. Pubmed: 8034709
  • Hayes GM, Carrigan PE, Beck AM, Miller LJ: Targeting the RNA splicing machinery as a novel treatment strategy for pancreatic carcinoma. Cancer Res. 2006 Apr 1;66(7):3819-27. Pubmed: 16585209
  • Hinek A, Smith AC, Cutiongco EM, Callahan JW, Gripp KW, Weksberg R: Decreased elastin deposition and high proliferation of fibroblasts from Costello syndrome are related to functional deficiency in the 67-kD elastin-binding protein. Am J Hum Genet. 2000 Mar;66(3):859-72. Pubmed: 10712202
  • Hooper JD, Nicol DL, Dickinson JL, Eyre HJ, Scarman AL, Normyle JF, Stuttgen MA, Douglas ML, Loveland KA, Sutherland GR, Antalis TM: Testisin, a new human serine proteinase expressed by premeiotic testicular germ cells and lost in testicular germ cell tumors. Cancer Res. 1999 Jul 1;59(13):3199-205. Pubmed: 10397266
  • Ishida-Takahashi R, Rosario F, Gong Y, Kopp K, Stancheva Z, Chen X, Feener EP, Myers MG Jr: Phosphorylation of Jak2 on Ser(523) inhibits Jak2-dependent leptin receptor signaling. Mol Cell Biol. 2006 Jun;26(11):4063-73. Pubmed: 16705160
  • Jones CM, Smith M, Henderson MJ: Reference data for cerebrospinal fluid and the utility of amino acid measurement for the diagnosis of inborn errors of metabolism. Ann Clin Biochem. 2006 Jan;43(Pt 1):63-6. Pubmed: 16390611
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • Khamzina L, Veilleux A, Bergeron S, Marette A: Increased activation of the mammalian target of rapamycin pathway in liver and skeletal muscle of obese rats: possible involvement in obesity-linked insulin resistance. Endocrinology. 2005 Mar;146(3):1473-81. Epub 2004 Dec 16. Pubmed: 15604215
  • Kim JK, Fillmore JJ, Sunshine MJ, Albrecht B, Higashimori T, Kim DW, Liu ZX, Soos TJ, Cline GW, O'Brien WR, Littman DR, Shulman GI: PKC-theta knockout mice are protected from fat-induced insulin resistance. J Clin Invest. 2004 Sep;114(6):823-7. Pubmed: 15372106
  • Lavker RM, Risse B, Brown H, Ginsburg D, Pearson J, Baker MS, Jensen PJ: Localization of plasminogen activator inhibitor type 2 (PAI-2) in hair and nail: implications for terminal differentiation. J Invest Dermatol. 1998 Jun;110(6):917-22. Pubmed: 9620299
  • Metzner L, Kottra G, Neubert K, Daniel H, Brandsch M: Serotonin, L-tryptophan, and tryptamine are effective inhibitors of the amino acid transport system PAT1. FASEB J. 2005 Sep;19(11):1468-73. Pubmed: 16126914
  • Morino K, Petersen KF, Dufour S, Befroy D, Frattini J, Shatzkes N, Neschen S, White MF, Bilz S, Sono S, Pypaert M, Shulman GI: Reduced mitochondrial density and increased IRS-1 serine phosphorylation in muscle of insulin-resistant offspring of type 2 diabetic parents. J Clin Invest. 2005 Dec;115(12):3587-93. Epub 2005 Nov 10. Pubmed: 16284649
  • Nagata Y, Higashi M, Ishii Y, Sano H, Tanigawa M, Nagata K, Noguchi K, Urade M: The presence of high concentrations of free D-amino acids in human saliva. Life Sci. 2006 Mar 6;78(15):1677-81. Epub 2006 Feb 9. Pubmed: 16480744
  • Nanda N, Bao M, Lin H, Clauser K, Komuves L, Quertermous T, Conley PB, Phillips DR, Hart MJ: Platelet endothelial aggregation receptor 1 (PEAR1), a novel epidermal growth factor repeat-containing transmembrane receptor, participates in platelet contact-induced activation. J Biol Chem. 2005 Jul 1;280(26):24680-9. Epub 2005 Apr 25. Pubmed: 15851471
  • Nuesch JP, Corbau R, Tattersall P, Rommelaere J: Biochemical activities of minute virus of mice nonstructural protein NS1 are modulated In vitro by the phosphorylation state of the polypeptide. J Virol. 1998 Oct;72(10):8002-12. Pubmed: 9733839
  • Olive PL, Banath JP, Sinnott LT: Phosphorylated histone H2AX in spheroids, tumors, and tissues of mice exposed to etoposide and 3-amino-1,2,4-benzotriazine-1,3-dioxide. Cancer Res. 2004 Aug 1;64(15):5363-9. Pubmed: 15289343
  • Paju A, Bjartell A, Zhang WM, Nordling S, Borgstrom A, Hansson J, Stenman UH: Expression and characterization of trypsinogen produced in the human male genital tract. Am J Pathol. 2000 Dec;157(6):2011-21. Pubmed: 11106574
  • Pfundt R, van Ruissen F, van Vlijmen-Willems IM, Alkemade HA, Zeeuwen PL, Jap PH, Dijkman H, Fransen J, Croes H, van Erp PE, Schalkwijk J: Constitutive and inducible expression of SKALP/elafin provides anti-elastase defense in human epithelia. J Clin Invest. 1996 Sep 15;98(6):1389-99. Pubmed: 8823304
  • Roesch PL, Redford P, Batchelet S, Moritz RL, Pellett S, Haugen BJ, Blattner FR, Welch RA: Uropathogenic Escherichia coli use d-serine deaminase to modulate infection of the murine urinary tract. Mol Microbiol. 2003 Jul;49(1):55-67. Pubmed: 12823810
  • Schultess J, Danielewski O, Smolenski AP: Rap1GAP2 is a new GTPase-activating protein of Rap1 expressed in human platelets. Blood. 2005 Apr 15;105(8):3185-92. Epub 2005 Jan 4. Pubmed: 15632203
  • Shafqat S, Tamarappoo BK, Kilberg MS, Puranam RS, McNamara JO, Guadano-Ferraz A, Fremeau RT Jr: Cloning and expression of a novel Na(+)-dependent neutral amino acid transporter structurally related to mammalian Na+/glutamate cotransporters. J Biol Chem. 1993 Jul 25;268(21):15351-5. Pubmed: 8340364
  • Stewart LV, Song K, Hsing AY, Danielpour D: Regulation of trespin expression by modulators of cell growth, differentiation, and apoptosis in prostatic epithelial cells. Exp Cell Res. 2003 Apr 1;284(2):303-15. Pubmed: 12651162
  • Strauss JF 3rd, Kallen CB, Christenson LK, Watari H, Devoto L, Arakane F, Kiriakidou M, Sugawara T: The steroidogenic acute regulatory protein (StAR): a window into the complexities of intracellular cholesterol trafficking. Recent Prog Horm Res. 1999;54:369-94; discussion 394-5. Pubmed: 10548884
  • Taniguchi A, Kataoka K, Kono T, Oseko F, Okuda H, Nagata I, Imura H: Parathyroid hormone-induced lipolysis in human adipose tissue. J Lipid Res. 1987 May;28(5):490-4. Pubmed: 3598394
  • Tsuei DJ, Hsu HC, Lee PH, Jeng YM, Pu YS, Chen CN, Lee YC, Chou WC, Chang CJ, Ni YH, Chang MH: RBMY, a male germ cell-specific RNA-binding protein, activated in human liver cancers and transforms rodent fibroblasts. Oncogene. 2004 Jul 29;23(34):5815-22. Pubmed: 15184870
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
  • Wyatt AW, Hussain A, Amann K, Klingel K, Kandolf R, Artunc F, Grahammer F, Huang DY, Vallon V, Kuhl D, Lang F: DOCA-induced phosphorylation of glycogen synthase kinase 3beta. Cell Physiol Biochem. 2006;17(3-4):137-44. Epub 2006 Mar 14. Pubmed: 16543730
  • Yu LY, Jokitalo E, Sun YF, Mehlen P, Lindholm D, Saarma M, Arumae U: GDNF-deprived sympathetic neurons die via a novel nonmitochondrial pathway. J Cell Biol. 2003 Dec 8;163(5):987-97. Epub 2003 Dec 1. Pubmed: 14657232
  • Zhu L, Wigle D, Hinek A, Kobayashi J, Ye C, Zuker M, Dodo H, Keeley FW, Rabinovitch M: The endogenous vascular elastase that governs development and progression of monocrotaline-induced pulmonary hypertension in rats is a novel enzyme related to the serine proteinase adipsin. J Clin Invest. 1994 Sep;94(3):1163-71. Pubmed: 8083356
Synthesis Reference: Zhu, Yanxin; Yuan, Minglong; Yuan, Mingwei; Du, Bilin; Zheng, Ling. Preparation of D-serine from acetylglycine. Faming Zhuanli Shenqing Gongkai Shuomingshu (2006), 4pp.
Material Safety Data Sheet (MSDS) Download (PDF)
External Links:
ResourceLink
CHEBI ID16523
HMDB IDHMDB03406
Pubchem Compound ID71077
Kegg IDC00740
ChemSpider ID64231
WikipediaDSN
BioCyc IDD-SERINE
EcoCyc IDD-SERINE
Ligand ExpoDSN

Enzymes

General function:
Involved in D-serine ammonia-lyase activity
Specific function:
D-serine = pyruvate + NH(3)
Gene Name:
dsdA
Locus Tag:
PA3357
Molecular weight:
48.2 kDa
Reactions
D-serine = pyruvate + NH(3).
General function:
Involved in oxidoreductase activity
Specific function:
Catalyzes the NADP-dependent oxidation of L-allo- threonine to L-2-amino-3-keto-butyrate, which is spontaneously decarboxylated into aminoacetone. Also acts on L-serine, D-serine, D-threonine, D-3-hydroxyisobutyrate, L-3-hydroxyisobutyrate, D- glycerate and L-glycerate
Gene Name:
ydfG
Locus Tag:
PA4907
Molecular weight:
27.4 kDa
Reactions
3-hydroxypropanoate + NADP(+) = 3-oxopropanoate + NADPH.

Transporters

General function:
Involved in nucleotide binding
Specific function:
Probably part of a binding-protein-dependent transport system yecCS for an amino acid. Probably responsible for energy coupling to the transport system
Gene Name:
yecC
Locus Tag:
PA5152
Molecular weight:
28.4 kDa
General function:
Involved in sodium:dicarboxylate symporter activity
Specific function:
Involved in the import of serine and threonine into the cell, with the concomitant import of sodium (symport system)
Gene Name:
sstT
Locus Tag:
PA2042
Molecular weight:
42.4 kDa