Record Information
Version2.0
Creation Date2012-05-31 13:58:54 -0600
Update Date2015-09-13 12:56:13 -0600
Secondary Accession Numbers
  • ECMDB03406
Identification
Name:D-Serine
DescriptionSerine 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
Weight:Average: 105.0926
Monoisotopic: 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
Description belongs to the class of organic compounds known as serine and derivatives. Serine and derivatives are compounds containing serine or a derivative thereof resulting from reaction of serine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentSerine and derivatives
Alternative Parents
Substituents
  • Serine or derivatives
  • Alpha-amino acid
  • D-alpha-amino acid
  • Beta-hydroxy acid
  • Hydroxy acid
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Alcohol
  • Primary amine
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Primary aliphatic amine
  • Organic oxide
  • Organopnictogen compound
  • Carbonyl group
  • Organic oxygen compound
  • Amine
  • Organic nitrogen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic 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 g/LALOGPS
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 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity22.04 m³·mol⁻¹ChemAxon
Polarizability9.39 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:
D-serine degradationPW002101 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-06sl-9000000000-033631650075b940e0e2View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-0089-9810000000-06fed7f6e260b107d95aView in MoNA
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, Positivesplash10-08g0-9300000000-dab8446816db786db171View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03dl-9000000000-1a5aef91299ef3583ca2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-9000000000-b6cfe52e68c644cacfd7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-6900000000-ee98a5a83ffbd434740eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0uki-9200000000-fa8d04d6ce99a290d187View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-05fu-9000000000-001b18464fb313594decView in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
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
Uniprot ID:
P00926
Molecular weight:
47900
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
Uniprot ID:
P39831
Molecular weight:
27249
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
Uniprot ID:
P37774
Molecular weight:
27677
General function:
Involved in transporter activity
Specific function:
Probably part of the binding-protein-dependent transport system yecCS for an amino acid; probably responsible for the translocation of the substrate across the membrane
Gene Name:
yecS
Uniprot ID:
P0AFT2
Molecular weight:
24801
General function:
Involved in gluconate transmembrane transporter activity
Specific function:
Probable permease for an unknown substrate
Gene Name:
dsdX
Uniprot ID:
P08555
Molecular weight:
47163
General function:
Involved in transporter activity
Specific function:
Involved in the import of serine into the cell. May be required for phage C1 adsorption by interacting with drcB. May also be involved in ampicillin sensitivity
Gene Name:
sdaC
Uniprot ID:
P0AAD6
Molecular weight:
46906
General function:
Involved in transporter activity
Specific function:
Involved in the import of threonine and serine into the cell, with the concomitant import of a proton (symport system)
Gene Name:
tdcC
Uniprot ID:
P0AAD8
Molecular weight:
48878
General function:
Involved in transport
Specific function:
Permease that is involved in the transport across the cytoplasmic membrane of D-alanine, D-serine and glycine
Gene Name:
cycA
Uniprot ID:
P0AAE0
Molecular weight:
51659
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
Uniprot ID:
P0AGE4
Molecular weight:
43477
General function:
Involved in transporter activity
Specific function:
Non-specific porin
Gene Name:
ompN
Uniprot ID:
P77747
Molecular weight:
41220
General function:
Involved in transporter activity
Specific function:
Uptake of inorganic phosphate, phosphorylated compounds, and some other negatively charged solutes
Gene Name:
phoE
Uniprot ID:
P02932
Molecular weight:
38922
General function:
Involved in transporter activity
Specific function:
OmpF is a porin that forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane. It is also a receptor for the bacteriophage T2
Gene Name:
ompF
Uniprot ID:
P02931
Molecular weight:
39333
General function:
Involved in transporter activity
Specific function:
Forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane
Gene Name:
ompC
Uniprot ID:
P06996
Molecular weight:
40368