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Human Metabolome Database Version 2.5

 

Showing metabocard for Phosphoserine (HMDB00272)

Legend: metabolite field enzyme field

Version 2.5
Creation Date 2005-11-16 15:48:42
Update Date 2009-05-05 20:57:49
Accession Number HMDB00272
Secondary Accession Numbers Not Available
Common Name Phosphoserine
Description The phosphoric acid ester of serine. As a constituent (residue) of proteins, its side chain can undergo O-linked glycosylation. This might be important in explaining some of the devastating consequences of diabetes. It is one of three amino acid residues that are commonly phosphorylated by kinases during cell signalling in eukaryotes. Phosphorylated serine residues are often referred to as phosphoserine. Serine proteases are a common type of protease. Serine, organic compound, one of the 20 amino acids commonly found in animal proteins. Only the L-stereoisomer appears in mammalian protein. It is not essential to the human diet, since it can be synthesized in the body from other metabolites, including glycine. Serine was first obtained from silk protein, a particularly rich source, in 1865. Its name is derived from the Latin for silk, sericum. Serine's structure was established in 1902.
Synonyms
  1. 3-O-Phosphoserine
  2. Dexfosfoserine
  3. Fosforina
  4. L-3-Phosphoserine
  5. L-O-Phosphoserine
  6. L-O-Serine phosphate
  7. L-Phosphoserine
  8. L-Serine dihydrogen phosphate (ester)
  9. L-Serine phosphate
  10. L-Serinephosphorate
  11. L-Serinephosphoric acid
  12. L-Seryl phosphate
Chemical IUPAC Name (2S)-2-amino-3-phosphonooxy-propanoic acid
Chemical Formula C3H8NO6P
Chemical Structure Structure
Chemical Taxonomy
Kingdom
  • Organic
Super Class
  • Amino acids and Amino Acid conjugates
Class
  • Amino Acid Phosphates
Sub Class
  • Proteotypic phospho-amino acids
Family
  • Mammalian Metabolite
Species
  • primary amine
  • primary aliphatic amine (alkylamine)
  • carboxylic acid
  • phosphoric acid ester
  • alpha-aminoacid
Biofunction
  • Component of Glycine, serine and threonine metabolism
Application
—
Source
  • Endogenous
Average Molecular Weight 185.072
Monoisotopic Molecular Weight 185.008926
Isomeric SMILES N[C@@H](COP(O)(O)=O)C(O)=O
Canonical SMILES NC(COP(O)(O)=O)C(O)=O
KEGG Compound ID C01005 Link Image
BioCyc ID 3-P-SERINE Link Image
BiGG ID Not Available
Wikipedia Link Phosphoserine Link Image
NuGOwiki Link HMDB00272 Link Image
Metagene Link HMDB00272 Link Image
METLIN ID 5270 Link Image
PubChem Compound 68841 Link Image
PubChem Substance 841619 Link Image
ChEBI ID 15811 Link Image
CAS Registry Number 407-41-0
InChI Identifier InChI=1/C3H8NO6P/c4-2(3(5)6)1-10-11(7,8)9/h2H,1,4H2,(H,5,6)(H2,7,8,9)/t2-/m0/s1
Synthesis Reference Barruel, Elena Mery. Biosynthesis of phosphoserine in vitro. Anales Fac. Quim. y Farm. (1960), 12 228-33.
Melting Point (Experimental) 170-171 oC
Experimental Water Solubility 71 mg/mL [HMP experimental] Source: PhysProp
Predicted Water Solubility 1000.0 mg/mL [MEYLAN,WM et al. (1996)]; 19.9 mg/mL [Predicted by ALOGPS] Calculated using ALOGPS
Physiological Charge -2
State Solid
Experimental LogP/Hydrophobicity Not Available Source: PhysProp
Predicted LogP/Hydrophobicity -2.32 [Predicted by ALOGPS]; -5.2 [Predicted by PubChem via XLOGP]; -4.54 [MEYLAN,WM & HOWARD,PH (1995)] Calculated using ALOGPS
Material Safety Data Sheet (MSDS)
MOL File Show
SDF File Show
PDB File Show
2D Structure
3D Structure
Experimental PDB ID 1B4G Link Image
Experimental PDB File Show
Experimental PDB Structure
Experimental 1H NMR Spectrum Download Spectrum
Download FID (Varian)
Show Experimental Conditions Link Image
Experimental 13C NMR Spectrum Not Available
Experimental 13C HSQC Spectrum Download Spectrum
Download FID (Bruker)
Show Experimental Conditions Link Image
Predicted 1H NMR Spectrum Show Image
Show Peaklist
Predicted 13C NMR Spectrum Show Image
Show Peaklist
Mass Spectrum
Low Energy
Download File
Show Experimental Conditions Link Image
Medium Energy
Download File
Show Experimental Conditions Link Image
High Energy
Download File
Show Experimental Conditions Link Image
Simplified TOCSY Spectrum Not Available
BMRB Spectrum Not Available
Cellular Location
  • Cytoplasm (Predicted from LogP)
Biofluid Location
  • Blood
  • Cerebrospinal Fluid
  • Urine
Tissue Location Not Available
Concentrations (Normal)
Biofluid Blood
Value 17.0 +/- 3.0 uM
Age Adult:>18 yrs old
Sex Female
Patient information Normal
Comments Not Available
References
  • Kang-Yoon SA, Kirksey A: Relation of short-term pyridoxine-HCl supplementation to plasma vitamin B-6 vitamers and amino acid concentrations in young women. Am J Clin Nutr. 1992 Apr;55(4):865-72. [PubMed Link Image]
Biofluid CSF
Value 4.2 +/- 1.7 uM
Age Adult:>18 yrs old
Sex Both
Patient information Normal
Comments Not Available
References
  • Geigy Scientific Tables, 8th Rev edition, pp. 165-177. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp., Basel, Switzerland c1981-1992.
Biofluid CSF
Value 5.0 +/- 0.9 uM
Age Adult:>18 yrs old
Sex Both
Patient information Normal
Comments Not Available
References
  • Molina JA, Jimenez-Jimenez FJ, Gomez P, Vargas C, Navarro JA, Orti-Pareja M, Gasalla T, Benito-Leon J, Bermejo F, Arenas J: Decreased cerebrospinal fluid levels of neutral and basic amino acids in patients with Parkinson's disease. J Neurol Sci. 1997 Sep 10;150(2):123-7. [PubMed Link Image]
Biofluid Urine
Value 4.605 (1.645-7.566) umol/mmol creatinine
Age Adult:>18 yrs old
Sex Both
Patient information Normal
Comments Not Available
References
  • Doctor's Data
Biofluid Urine
Value 2.0 (0.53-3.28) umol/mmol creatinine
Age Adult:>18 yrs old
Sex Both
Patient information Normal
Comments Not Available
References
  • Gatti R, Gioia MG: Liquid chromatographic fluorescence determination of amino acids in plasma and urine after derivatization with phanquinone. Biomed Chromatogr. 2008 Feb;22(2):207-13. [PubMed Link Image]
Biofluid Urine
Value 6.0 (2.71-10.4) umol/mmol creatinine
Age Adult:>18 yrs old
Sex Both
Patient information Normal
Comments Not Available
References
  • Gatti R, Gioia MG: Liquid chromatographic fluorescence determination of amino acids in plasma and urine after derivatization with phanquinone. Biomed Chromatogr. 2008 Feb;22(2):207-13. [PubMed Link Image]
Concentrations (Abnormal) Not Available
Associated Disorders Not Available
OMIM ID Not Available
Pathways
Name SMPDB Link KEGG Link
Glycine and Serine Metabolism SMP00004 Link Image map00260 Link Image
General References
  1. Molina JA, Jimenez-Jimenez FJ, Gomez P, Vargas C, Navarro JA, Orti-Pareja M, Gasalla T, Benito-Leon J, Bermejo F, Arenas J: Decreased cerebrospinal fluid levels of neutral and basic amino acids in patients with Parkinson's disease. J Neurol Sci. 1997 Sep 10;150(2):123-7. [PubMed Link Image]
  2. Wikipedia Link Image
Metabolic Enzymes
  1. Phosphoserine phosphatase
  2. Phosphoserine aminotransferase 1
  3. cDNA, FLJ96235, Homo sapiens phosphoserine phosphatase (PSPH), mRNA (Phosphoserine phosphatase, isoform CRA_a)
Enzyme 1 [top]
Enzyme 1 ID 6169
Enzyme 1 Name Phosphoserine phosphatase
Enzyme 1 Synonyms
  1. PSP
  2. O-phosphoserine phosphohydrolase
  3. PSPase
  4. L-3-phosphoserine phosphatase
Enzyme 1 Gene Name PSPH
Enzyme 1 Protein Sequence >Phosphoserine phosphatase 
MVSHSELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAVSEMTRRAMGGAVPFKA
ALTERLALIQPSREQVQRLIAEQPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVA
SKLNIPATNVFANRLKFYFNGEYAGFDETQPTAESGGKGKVIKLLKEKFHFKKIIMIGDG
ATDMEACPPADAFIGFGGNVIRQQVKDNAKWYITDFVELLGELEE
Enzyme 1 Number of Residues 225
Enzyme 1 Molecular Weight 25008
Enzyme 1 Theoretical pI 5.42
Enzyme 1 GO Classification
Function
  • catalytic activity
  • hydrolase activity
  • hydrolase activity, acting on ester bonds
  • phosphoric ester hydrolase activity
  • phosphoric monoester hydrolase activity
  • phosphoserine phosphatase activity
Process
  • L-serine biosynthesis
  • L-serine metabolism
  • amino acid and derivative metabolism
  • amino acid metabolism
  • cellular metabolism
  • metabolism
  • physiological process
  • serine family amino acid metabolism
Component
—
Enzyme 1 General Function Amino acid transport and metabolism
Enzyme 1 Specific Function Catalyzes the last step in the biosynthesis of serine from carbohydrates. The reaction mechanism proceeds via the formation of a phosphoryl-enzyme intermediates
Enzyme 1 Pathways
  • Glycine, Serine and Threonine Metabolism (map00260 Link Image)
Enzyme 1 Reactions
  • L(or D)-O-phosphoserine + H2O = L(or D)-serine + phosphate
Enzyme 1 Pfam Domain Function
Enzyme 1 Signals
  • None
Enzyme 1 Transmembrane Regions
  • None
Enzyme 1 Essentiality Not Available
Enzyme 1 GenBank ID Protein 1890331 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID P78330 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name SERB_HUMAN Link Image
Enzyme 1 PDB ID 1NNL Link Image
Enzyme 1 PDB File Show
Enzyme 1 3D Structure
Enzyme 1 Cellular Location Not Available
Enzyme 1 Gene Sequence >678 bp 
ATGGTCTCCCACTCAGAGCTGAGGAAGCTTTTCTACTCAGCAGATGCTGTGTGTTTTGAT
GTTGACAGCACGGTCATCAGAGAAGAAGGAATCGATGAGCTAGCCAAAATCTGTGGCGTT
GAGGACGCGGTGTCAGAAATGACACGGCGAGCCATGGGCGGGGCAGTGCCTTTCAAAGCT
GCTCTCACAGAGCGCTTAGCCCTCATCCAGCCCTCCAGGGAGCAGGTGCAGAGACTCATA
GCAGAGCAACCCCCACACCTGACCCCCGGCATAAGGGAGCTGGTAAGTCGCCTACAGGAG
CGAAATGTTCAGGTTTTCCTAATATCTGGTGGCTTTAGGAGTATTGTAGAGCATGTTGCT
TCAAAGCTCAATATCCCAGCAACCAATGTATTTGCCAATAGGCTGAAATTCTACTTTAAC
GGTGAATATGCAGGTTTTGATGAGACGCAGCCAACAGCTGAATCTGGTGGAAAAGGAAAA
GTGATTAAACTTTTAAAGGAAAAATTTCATTTTAAGAAAATAATCATGATTGGAGATGGT
GCCACAGATATGGAAGCCTGTCCTCCTGCTGATGCTTTCATTGGATTTGGAGGAAATGTG
ATCAGGCAACAAGTCAAGGATAACGCCAAATGGTATATCACTGATTTTGTAGAGCTGCTG
GGAGAACTGGAAGAATAA
Enzyme 1 GenBank Gene ID Y10275 Link Image
Enzyme 1 GeneCard ID PSPH Link Image
Enzyme 1 GenAtlas ID PSPH Link Image
Enzyme 1 HGNC ID HGNC:9577 Link Image
Enzyme 1 Chromosome Location 7
Enzyme 1 Locus 7p15.2-p15.1
Enzyme 1 SNPs SNPJam Report Link Image
Enzyme 1 General References
  1. Collet JF, Gerin I, Rider MH, Veiga-da-Cunha M, Van Schaftingen E: Human L-3-phosphoserine phosphatase: sequence, expression and evidence for a phosphoenzyme intermediate. FEBS Lett. 1997 May 26;408(3):281-4. [PubMed Link Image]
Enzyme 1 Metabolite References Not Available
Enzyme 2 [top]
Enzyme 2 ID 13053
Enzyme 2 Name Phosphoserine aminotransferase 1
Enzyme 2 Synonyms
  1. Phosphoserine aminotransferase 1, isoform CRA_a
Enzyme 2 Gene Name PSAT1
Enzyme 2 Protein Sequence >Phosphoserine aminotransferase 1 
MDAPRQVVNFGPGPAKLPHSVLLEIQKELLDYKGVGISVLEMSHRSSDFAKIINNTENLV
RELLAVPDNYKVIFLQGGGCGQFSAVPLNLIGLKAGRCADYVVTGAWSAKAAEEAKKFGT
INIVHPKLGSYTKIPDPSTWNLNPDASYVYYCANETVHGVEFDFIPDVKGAVLVCDMSSN
FLSKPVDVSKFGVIFAGAQKNVGSAGVTVVIVRDDLLGFALRECPSVLEYKVQAGNSSLY
NTPPCFSIYVMGLVLEWIKNNGGAAAMEKLSSIKSQTIYEIIDNSQGFYVSVGGIRASLY
NAVTIEDVQKLAAFMKKFLEMHQL
Enzyme 2 Number of Residues 324
Enzyme 2 Molecular Weight 35189
Enzyme 2 Theoretical pI 6.66
Enzyme 2 GO Classification
Function
  • catalytic activity
  • transaminase activity
  • transferase activity
  • transferase activity, transferring nitrogenous groups
Process
  • L-serine biosynthesis
  • L-serine metabolism
  • amino acid and derivative metabolism
  • amino acid metabolism
  • cellular metabolism
  • metabolism
  • physiological process
  • serine family amino acid metabolism
Component
—
Enzyme 2 General Function Coenzyme transport and metabolism
Enzyme 2 Specific Function Not Available
Enzyme 2 Pathways Not Available
Enzyme 2 Reactions Not Available
Enzyme 2 Pfam Domain Function
Enzyme 2 Signals
  • None
Enzyme 2 Transmembrane Regions
  • None
Enzyme 2 Essentiality Not Available
Enzyme 2 GenBank ID Protein Not Available
Enzyme 2 UniProtKB/Swiss-Prot ID Q5T7G5 Link Image
Enzyme 2 UniProtKB/Swiss-Prot Entry Name Q5T7G5_HUMAN Link Image
Enzyme 2 PDB ID Not Available
Enzyme 2 Cellular Location Not Available
Enzyme 2 Gene Sequence Not Available
Enzyme 2 GenBank Gene ID AL353594 Link Image
Enzyme 2 GeneCard ID Q5T7G5 Link Image
Enzyme 2 GenAtlas ID PSAT1 Link Image
Enzyme 2 HGNC ID HGNC:19129 Link Image
Enzyme 2 Chromosome Location Not Available
Enzyme 2 Locus Not Available
Enzyme 2 SNPs SNPJam Report Link Image
Enzyme 2 General References Not Available
Enzyme 2 Metabolite References Not Available
Enzyme 3 [top]
Enzyme 3 ID 16507
Enzyme 3 Name cDNA, FLJ96235, Homo sapiens phosphoserine phosphatase (PSPH), mRNA (Phosphoserine phosphatase, isoform CRA_a)
Enzyme 3 Synonyms Not Available
Enzyme 3 Gene Name PSPH
Enzyme 3 Protein Sequence >cDNA, FLJ96235, Homo sapiens phosphoserine phosphatase (PSPH), mRNA (Phosphoserine phosphatase, isoform CRA_a) 
MVSHSELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAVSEMTRRAMGGAVPFKA
ALTERLALIQPSREQVQRLIAEQPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVA
SKLNIPATNVFANRLKFYFNGEYAGFDETQPTAESGGKGKVIKLLKEKFHFKKIIMIGDG
ATDMEACPPADAFIGFGGNVIRQQVKDNAKWYITDFVELLGELEE
Enzyme 3 Number of Residues 225
Enzyme 3 Molecular Weight 25008
Enzyme 3 Theoretical pI 5.42
Enzyme 3 GO Classification
Function
  • catalytic activity
  • hydrolase activity
  • hydrolase activity, acting on ester bonds
  • phosphoric ester hydrolase activity
  • phosphoric monoester hydrolase activity
  • phosphoserine phosphatase activity
Process
  • L-serine biosynthesis
  • L-serine metabolism
  • amino acid and derivative metabolism
  • amino acid metabolism
  • cellular metabolism
  • metabolism
  • physiological process
  • serine family amino acid metabolism
Component
—
Enzyme 3 General Function Amino acid transport and metabolism
Enzyme 3 Specific Function Not Available
Enzyme 3 Pathways Not Available
Enzyme 3 Reactions Not Available
Enzyme 3 Pfam Domain Function
Enzyme 3 Signals
  • None
Enzyme 3 Transmembrane Regions
  • None
Enzyme 3 Essentiality Not Available
Enzyme 3 GenBank ID Protein Not Available
Enzyme 3 UniProtKB/Swiss-Prot ID B2RCR5 Link Image
Enzyme 3 UniProtKB/Swiss-Prot Entry Name B2RCR5_HUMAN Link Image
Enzyme 3 PDB ID 1NNL Link Image
Enzyme 3 PDB File Show
Enzyme 3 3D Structure
Enzyme 3 Cellular Location Not Available
Enzyme 3 Gene Sequence Not Available
Enzyme 3 GenBank Gene ID AK315235 Link Image
Enzyme 3 GeneCard ID B2RCR5 Link Image
Enzyme 3 GenAtlas ID Not Available
Enzyme 3 HGNC ID Not Available
Enzyme 3 Chromosome Location Not Available
Enzyme 3 Locus Not Available
Enzyme 3 SNPs SNPJam Report Link Image
Enzyme 3 General References Not Available
Enzyme 3 Metabolite References Not Available