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Human Metabolome Database Version 2.5

 

Showing metabocard for D-Ornithine (HMDB03374)

Legend: metabolite field enzyme field

Version 2.5
Creation Date 2006-08-12 20:50:22
Update Date 2009-07-30 11:29:05
Accession Number HMDB03374
Secondary Accession Numbers Not Available
Common Name D-Ornithine
Description An amino acid produced in the urea cycle by the splitting off of urea from arginine. Ornithine is one of the products of the action of the enzyme arginase on L-arginine, creating urea. Therefore, ornithine is a central part of the urea cycle, which allows for the disposal of excess nitrogen.
Synonyms
  1. (2R)-2,5-diaminopentanoate
  2. (2R)-2,5-diaminopentanoic acid
  3. (R)-ornithine
  4. ornithine
Chemical IUPAC Name (2R)-2,5-diaminopentanoic acid
Chemical Formula C5H12N2O2
Chemical Structure Structure
Chemical Taxonomy
Kingdom
  • Organic
Super Class
  • Amino acids and Amino Acid conjugates
Class
  • Amino Acids
Sub Class
  • NA
Family
  • Mammalian Metabolite
Species
  • primary amine
  • primary aliphatic amine (alkylamine)
  • carboxylic acid
  • alpha-aminoacid
Biofunction
  • Component of Arginine and proline metabolism
Application
—
Source
  • Endogenous
Average Molecular Weight 132.161
Monoisotopic Molecular Weight 132.089874
Isomeric SMILES NCCC[C@@H](N)C(O)=O
Canonical SMILES NCCCC(N)C(O)=O
KEGG Compound ID C00515 Link Image
BioCyc ID CPD-217 Link Image
BiGG ID 2263101 Link Image
Wikipedia Link ornithine Link Image
NuGOwiki Link HMDB03374 Link Image
Metagene Link HMDB03374 Link Image
METLIN ID 6910 Link Image
PubChem Compound 71082 Link Image
PubChem Substance 589770 Link Image
ChEBI ID 16176 Link Image
CAS Registry Number 348-66-3
InChI Identifier InChI=1/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m1/s1
Synthesis Reference Furui, Masakatsu; Takahashi, Eiji; Shibatani, Takeji. Microbial manufacture of D-amino acids from racemates. Jpn. Kokai Tokkyo Koho (1998), 13 pp.
Melting Point (Experimental) Not Available
Experimental Water Solubility Not Available Source: PhysProp
Predicted Water Solubility 172.0 mg/mL [Predicted by ALOGPS] Calculated using ALOGPS
Physiological Charge 1
State Solid
Experimental LogP/Hydrophobicity Not Available Source: PhysProp
Predicted LogP/Hydrophobicity -3.64 [Predicted by ALOGPS]; -3.3 [Predicted by PubChem via XLOGP] Calculated using ALOGPS
Material Safety Data Sheet (MSDS)
MOL File Show
SDF File Show
PDB File Show
2D Structure
3D Structure
Experimental PDB ID Not Available
Experimental 1H NMR Spectrum Not Available
Experimental 13C NMR Spectrum Not Available
Experimental 13C HSQC Spectrum Not Available
Predicted 1H NMR Spectrum Show Image
Show Peaklist
Predicted 13C NMR Spectrum Show Image
Show Peaklist
Mass Spectrum Not Available
Simplified TOCSY Spectrum Not Available
BMRB Spectrum Not Available
Cellular Location
  • Cytoplasm (Predicted from LogP)
  • peroxisome
Biofluid Location
  • Blood
Tissue Location
Tissue References
Fibroblasts —
Intestine —
Liver —
Muscle —
Skeletal Muscle —
Skin —
Spleen —
Concentrations (Normal)
Biofluid Blood
Value 89.0 +/- 28.0 uM
Age Adult:>18 yrs old
Sex Both
Patient information After arginine-free diet
Comments Not Available
References
  • Pita AM, Fernandez-Bustos A, Rodes M, Arranz JA, Fisac C, Virgili N, Soler J, Wakabayashi Y: Orotic aciduria and plasma urea cycle-related amino acid alterations in short bowel syndrome, evoked by an arginine-free diet. JPEN J Parenter Enteral Nutr. 2004 Sep-Oct;28(5):315-23. [PubMed Link Image]
Concentrations (Abnormal)
Biofluid Blood
Value 62.0 +/- 28.0 uM
Age Adult:>18 yrs old
Sex Both
Condition Short bowel syndrome
Comments After arginine-free diet
References
  • Pita AM, Fernandez-Bustos A, Rodes M, Arranz JA, Fisac C, Virgili N, Soler J, Wakabayashi Y: Orotic aciduria and plasma urea cycle-related amino acid alterations in short bowel syndrome, evoked by an arginine-free diet. JPEN J Parenter Enteral Nutr. 2004 Sep-Oct;28(5):315-23. [PubMed Link Image]
Associated Disorders
Condition References
Short bowel syndrome
  • Pita AM, Fernandez-Bustos A, Rodes M, Arranz JA, Fisac C, Virgili N, Soler J, Wakabayashi Y: Orotic aciduria and plasma urea cycle-related amino acid alterations in short bowel syndrome, evoked by an arginine-free diet. JPEN J Parenter Enteral Nutr. 2004 Sep-Oct;28(5):315-23. [PubMed Link Image]
OMIM ID Not Available
Pathways
Name SMPDB Link KEGG Link
D-Arginine and D-Ornithine Metabolism SMP00036 Link Image map00472 Link Image
General References
  1. Deignan JL, Livesay JC, Yoo PK, Goodman SI, O'Brien WE, Iyer RK, Cederbaum SD, Grody WW: Ornithine deficiency in the arginase double knockout mouse. Mol Genet Metab. 2006 Sep-Oct;89(1-2):87-96. Epub 2006 Jun 5. [PubMed Link Image]
  2. Mayer UM: [Hyperornithinaemia in patients with retinal dystrophy] Ophthalmologe. 2003 Jan;100(1):55-61. [PubMed Link Image]
  3. Filho JC, Bergstrom J, Stehle P, Furst P: Simultaneous measurements of free amino acid patternsof plasma, muscle and erythrocytes in healthy human subjects. Clin Nutr. 1997 Dec;16(6):299-305. [PubMed Link Image]
  4. Lauteala T, Mykkanen J, Sperandeo MP, Gasparini P, Savontaus ML, Simell O, Andria G, Sebastio G, Aula P: Genetic homogeneity of lysinuric protein intolerance. Eur J Hum Genet. 1998 Nov-Dec;6(6):612-5. [PubMed Link Image]
  5. Saito A, Noguchi Y, Yoshikawa T, Doi C, Fukuzawa K, Matsumoto A, Ito T, Tsuburaya A, Nagahara N: Gastrectomized patients are in a state of chronic protein malnutrition analyses of 23 amino acids. Hepatogastroenterology. 2001 Mar-Apr;48(38):585-9. [PubMed Link Image]
  6. Nefyodov LI, Uglyanitsa KN, Smirnov VY, Karavay AV, Brzosko W: Comparative evaluation of blood plasma and tumor tissue amino acid pool in radiation or neoadjuvant preoperative therapies of breast cancer with the antitumor drug Ukrain. Drugs Exp Clin Res. 2000;26(5-6):231-7. [PubMed Link Image]
  7. Rutten EP, Engelen MP, Schols AM, Deutz NE: Skeletal muscle glutamate metabolism in health and disease: state of the art. Curr Opin Clin Nutr Metab Care. 2005 Jan;8(1):41-51. [PubMed Link Image]
  8. Vella S, Steiner F, Schlumbom V, Zurbrugg R, Wiesmann UN, Schaffner T, Wermuth B: Mutation of ornithine transcarbamylase (H136R) in a girl with severe intermittent orotic aciduria but normal enzyme activity. J Inherit Metab Dis. 1997 Aug;20(4):517-24. [PubMed Link Image]
  9. Sela BA, Zlotnik J, Masos T, Yablonski G, Abraham F: [Gyrate atrophy of choroid and retina, and hyperornithinemia] Harefuah. 2000 Jan 16;138(2):101-5, 175. [PubMed Link Image]
  10. Camacho JA, Rioseco-Camacho N, Andrade D, Porter J, Kong J: Cloning and characterization of human ORNT2: a second mitochondrial ornithine transporter that can rescue a defective ORNT1 in patients with the hyperornithinemia-hyperammonemia-homocitrullinuria syndrome, a urea cycle disorder. Mol Genet Metab. 2003 Aug;79(4):257-71. [PubMed Link Image]
  11. Monnier VM, Sell DR: Prevention and repair of protein damage by the Maillard reaction in vivo. Rejuvenation Res. 2006 Summer;9(2):264-73. [PubMed Link Image]
  12. Zhang X, Rimpilainen M, Hoffmann B, Simelyte E, Aho H, Toivanen P: Experimental chronic arthritis and granulomatous inflammation induced by bifidobacterium cell walls. Scand J Immunol. 2001 Jul-Aug;54(1-2):171-9. [PubMed Link Image]
  13. Jensen TG, Sullivan DM, Morgan RA, Taichman LB, Nussenblatt RB, Blaese RM, Csaky KG: Retrovirus-mediated gene transfer of ornithine-delta-aminotransferase into keratinocytes from gyrate atrophy patients. Hum Gene Ther. 1997 Nov 20;8(17):2125-32. [PubMed Link Image]
  14. Sell DR, Monnier VM: Ornithine is a novel amino acid and a marker of arginine damage by oxoaldehydes in senescent proteins. Ann N Y Acad Sci. 2005 Jun;1043:118-28. [PubMed Link Image]
  15. Gokmen SS, Aygit AC, Ayhan MS, Yorulmaz F, Gulen S: Significance of arginase and ornithine in malignant tumors of the human skin. J Lab Clin Med. 2001 May;137(5):340-4. [PubMed Link Image]
  16. Wikipedia Link Image
Metabolic Enzymes
  1. D-amino-acid oxidase
  2. cDNA, FLJ93456, highly similar to Homo sapiens D-amino-acid oxidase (DAO), mRNA (D-amino-acid oxidase, isoform CRA_c)
Enzyme 1 [top]
Enzyme 1 ID 5438
Enzyme 1 Name D-amino-acid oxidase
Enzyme 1 Synonyms
  1. DAMOX
  2. DAO
  3. DAAO
Enzyme 1 Gene Name DAO
Enzyme 1 Protein Sequence >D-amino-acid oxidase 
MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLSDPN
NPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPR
ELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVN
CTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPYIIPGTQTVTLGG
IFQLGNWSELNNIQDHNTIWEGCCRLEPTLKNARIIGERTGFRPVRPQIRLEREQLRTGP
SNTEVIHNYGHGGYGLTIHWGCALEAAKLFGRILEEKKLSRMPPSHL
Enzyme 1 Number of Residues 347
Enzyme 1 Molecular Weight 39475
Enzyme 1 Theoretical pI 6.84
Enzyme 1 GO Classification
Function
  • D-amino-acid oxidase activity
  • catalytic activity
  • oxidoreductase activity
  • oxidoreductase activity, acting on the CH-NH2 group of donors
  • oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
Process
  • cellular metabolism
  • electron transport
  • generation of precursor metabolites and energy
  • metabolism
  • physiological process
Component
—
Enzyme 1 General Function Amino acid transport and metabolism
Enzyme 1 Specific Function Could act as a detoxifying agent which removes D-amino acids accumulated during aging. Acts on a variety of D-amino acids with a preference for those having small hydrophobic side chains followed by those bearing polar, aromatic, and basic groups. Does not act on acidic amino acids
Enzyme 1 Pathways
  • Arginine and Proline Metabolism (map00330 Link Image)
  • D-Arginine and D-ornithine Metabolism (map00472 Link Image)
  • Glycine, Serine and Threonine Metabolism (map00260 Link Image)
Enzyme 1 Reactions
  • a D-amino acid + H2O + O2 = a 2-oxo acid + ammonia + H2O2
Enzyme 1 Pfam Domain Function
Enzyme 1 Signals
  • 1-16
Enzyme 1 Transmembrane Regions Not Available
Enzyme 1 Essentiality Not Available
Enzyme 1 GenBank ID Protein 30446 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID P14920 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name OXDA_HUMAN Link Image
Enzyme 1 PDB ID Not Available
Enzyme 1 Cellular Location Not Available
Enzyme 1 Gene Sequence >1044 bp 
ATGCGTGTGGTGGTGATTGGAGCAGGAGTCATCGGGCTGTCCACCGCCCTCTGCATCCAT
GAGCGCTACCACTCAGTCCTGCAGCCACTGCACATAAAGGTCTACGCGGACCGCTTCACC
CCACTCACCACCACCGACGTGGCTGCCGGCCTCTGGCAGCCCTACCTTTCTGACCCCAAC
AACCCACAGGAGGCGGACTGGAGCCAACAGACCTTTGACTATCTCCTGAGCCATGTCCAT
TCTCCCAACGCTGAAAACCTGGGCCTGTTCCTAATCTCGGGCTACAACCTCTTCCATGAA
GCCATTCCGGACCCTTCCTGGAAGGACACAGTTCTGGGATTTCGGAAGCTGACCCCCAGA
GAGCTGGATATGTTCCCAGATTACGGCTATGGCTGGTTCCACACAAGCCTAATTCTGGAG
GGAAAGAACTATCTACAGTGGCTGACTGAAAGGTTAACTGAGAGGGGAGTGAAGTTCTTC
CAGCGGAAAGTGGAGTCTTTTGAGGAGGTGGCAAGAGAAGGCGCAGACGTGATTGTCAAC
TGCACTGGGGTATGGGCTGGGGCGCTACAACGAGACCCCCTGCTGCAGCCAGGCCGGGGG
CAGATCATGAAGGTGGACGCCCCTTGGATGAAGCACTTCATTCTCACCCATGACCCAGAG
AGAGGCATCTACAATTCCCCGTACATCATCCCAGGGACCCAGACAGTTACTCTTGGAGGC
ATCTTCCAGTTGGGAAACTGGAGTGAACTAAACAATATCCAGGACCACAACACCATTTGG
GAAGGCTGCTGCAGACTGGAGCCCACACTGAAGAATGCAAGAATTATTGGTGAAGCAACT
GGCTTCCGGCCAGTACGCCCCCAGATTCGGCTAGAAAGAGAACAGCTTCGCACTGGACCT
TCAAACACAGAGGTCATCCACAACTATGGCCATGGAGGCTACGGGCTCACCATCCACTGG
GGATGTGCCCTGGAGGCAGCCAAGCTCTTTGGGAGAATCCTGGAAGAAAAGAAATTGTCC
AGAATGCCACCATCCCACCTCTGA
Enzyme 1 GenBank Gene ID X13227 Link Image
Enzyme 1 GeneCard ID DAO Link Image
Enzyme 1 GenAtlas ID DAO Link Image
Enzyme 1 HGNC ID HGNC:2671 Link Image
Enzyme 1 Chromosome Location 12
Enzyme 1 Locus 12q24
Enzyme 1 SNPs SNPJam Report Link Image
Enzyme 1 General References
  1. Momoi K, Fukui K, Watanabe F, Miyake Y: Molecular cloning and sequence analysis of cDNA encoding human kidney D-amino acid oxidase. FEBS Lett. 1988 Sep 26;238(1):180-4. [PubMed Link Image]
  2. Fukui K, Miyake Y: Molecular cloning and chromosomal localization of a human gene encoding D-amino-acid oxidase. J Biol Chem. 1992 Sep 15;267(26):18631-8. [PubMed Link Image]
Enzyme 1 Metabolite References Not Available
Enzyme 2 [top]
Enzyme 2 ID 16461
Enzyme 2 Name cDNA, FLJ93456, highly similar to Homo sapiens D-amino-acid oxidase (DAO), mRNA (D-amino-acid oxidase, isoform CRA_c)
Enzyme 2 Synonyms Not Available
Enzyme 2 Gene Name DAO
Enzyme 2 Protein Sequence >cDNA, FLJ93456, highly similar to Homo sapiens D-amino-acid oxidase (DAO), mRNA (D-amino-acid oxidase, isoform CRA_c) 
MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLSDPN
NPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPR
ELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVN
CTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPYIIPGTQTVTLGG
IFQLGNWSELNNIQDHNTIWEGCCRLEPTLKNARIIGERTGFRPVRPQIRLEREQLRTGP
SNTEVIHNYGHGGYGLTIHWGCALEAAKLFGRILEEKKLSRMPPSHL
Enzyme 2 Number of Residues 347
Enzyme 2 Molecular Weight 39475
Enzyme 2 Theoretical pI 6.84
Enzyme 2 GO Classification
Function
  • ATP binding
  • D-amino-acid oxidase activity
  • RNA ligase activity
  • adenyl nucleotide binding
  • binding
  • catalytic activity
  • ligase activity
  • ligase activity, forming phosphoric ester bonds
  • nucleotide binding
  • oxidoreductase activity
  • oxidoreductase activity, acting on the CH-NH2 group of donors
  • oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
  • purine nucleotide binding
  • tRNA ligase activity
Process
  • RNA metabolism
  • cellular metabolism
  • electron transport
  • generation of precursor metabolites and energy
  • metabolism
  • nucleobase, nucleoside, nucleotide and nucleic acid metabolism
  • physiological process
  • tRNA aminoacylation
  • tRNA aminoacylation for protein translation
  • tRNA metabolism
Component
—
Enzyme 2 General Function Amino acid 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 B2R7I5 Link Image
Enzyme 2 UniProtKB/Swiss-Prot Entry Name B2R7I5_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 AK312995 Link Image
Enzyme 2 GeneCard ID B2R7I5 Link Image
Enzyme 2 GenAtlas ID Not Available
Enzyme 2 HGNC ID Not Available
Enzyme 2 Chromosome Location 12
Enzyme 2 Locus 12q24
Enzyme 2 SNPs SNPJam Report Link Image
Enzyme 2 General References Not Available
Enzyme 2 Metabolite References Not Available