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Human Metabolome Database Version 3.5

Showing metabocard for Ornithine (HMDB00214)

• Identification
• Taxonomy
• Ontology
• Physical properties
• Spectra
• Biological properties
• Concentrations
• Links
• References

enzymes (19)

• Blood
• Urine

Record Information
Version	3.5
Creation Date	2005-11-16 08:48:42 -0700
Update Date	2013-02-08 17:08:05 -0700
HMDB ID	HMDB00214
Secondary Accession Numbers	HMDB00818 HMDB04984
Metabolite Identification
Common Name	Ornithine
Description	Ornithine is an amino acid produced in the urea cycle by the splitting off of urea from arginine. It is a central part of the urea cycle, which allows for the disposal of excess nitrogen. L-Ornithine is also a precursor of citrulline and arginine. In order for ornithine produced in the cytosol to be converted to citrulline, it must first cross the inner mitochondrial membrane into the mitochondrial matrix where it is carbamylated by ornithine transcarbamylase. This transfer is mediated by the mitochondrial ornithine transporter (SLC25A15; AF112968; ORNT1). Mutations in the mitochondrial ornithine transporter result in hyperammonemia, hyperornithinemia, homocitrullinuria (HHH) syndrome, a disorder of the urea cycle. (PMID 16256388 ) The pathophysiology of the disease may involve diminished ornithine transport into mitochondria, resulting in ornithine accumulation in the cytoplasm and reduced ability to clear carbamoyl phosphate and ammonia loads. (OMIM 838970 ).
Structure	Download: MOL | SDF | SMILES | InChI Display: 2D Structure | 3D Structure
Synonyms	(+)-S-Ornithine (S)-2,5-Diaminopentanoate (S)-2,5-Diaminopentanoic acid (S)-a,D-Diaminovalerate (S)-a,D-Diaminovaleric acid (S)-Ornithine 5-Amino-L-Norvaline L-(-)-Ornithine L-Ornithine
Chemical Formula	C5H12N2O2
Average Molecular Weight	132.161
Monoisotopic Molecular Weight	132.089877638
IUPAC Name	(2S)-2,5-diaminopentanoic acid
Traditional IUPAC Name	L-ornithine
CAS Registry Number	70-26-8
SMILES	NCCC[C@H](N)C(O)=O
InChI Identifier	InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1
InChI Key	AHLPHDHHMVZTML-BYPYZUCNSA-N
Chemical Taxonomy
Kingdom	Organic Compounds
Super Class	Amino Acids, Peptides, and Analogues
Class	Amino Acids and Derivatives
Sub Class	Alpha Amino Acids and Derivatives
Other Descriptors	Aliphatic Acyclic Compounds alpha-amino acid(ChEBI)
Substituents	Carboxylic Acid Polyamine Primary Aliphatic Amine (Alkylamine)
Direct Parent	Alpha Amino Acids and Derivatives
Ontology
Status	Detected and Quantified
Origin	Endogenous
Biofunction	Component of Arginine and proline metabolism Component of Glycine, serine and threonine metabolism
Application	Not Available
Cellular locations	Extracellular Mitochondria
Physical Properties
State	Solid
Experimental Properties	Property Value Reference Melting Point 140 °C Not Available Boiling Point Not Available Not Available Water Solubility 620 mg/mL Not Available LogP -4.22 SANGSTER (1994)
Predicted Properties	Property Value Source Water Solubility 172 g/L ALOGPS LogP -3.64 ALOGPS LogP -3.7 ChemAxon LogS 0.11 ALOGPS pKa (strongest acidic) 2.67 ChemAxon pKa (strongest basic) 10.29 ChemAxon Hydrogen Acceptor Count 4 ChemAxon Hydrogen Donor Count 3 ChemAxon Polar Surface Area 89.34 A2 ChemAxon Rotatable Bond Count 4 ChemAxon Refractivity 33.21 ChemAxon Polarizability 13.94 ChemAxon Formal Charge 0 ChemAxon Physiological Charge 1 ChemAxon
Spectra
	Gas-MS Spectrum 1H NMR Spectrum 13C NMR Spectrum MS/MS Spectrum Quattro_QQQ 10 MS/MS Spectrum Quattro_QQQ 25 MS/MS Spectrum Quattro_QQQ 40 MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 10 [1H,1H] 2D NMR Spectrum [1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations	Extracellular Mitochondria
Biofluid Locations	Blood Cerebrospinal Fluid (CSF) Saliva Urine
Tissue Location	Liver Prostate Skin Gut
Pathways	Name SMPDB Link KEGG Link Arginine and Proline Metabolism SMP00020 map00330 Urea Cycle SMP00059 map00330 Spermidine and Spermine Biosynthesis SMP00445 Not Available Glycine and Serine Metabolism SMP00004 map00260
Normal Concentrations
	Biofluid Status Value Age Sex Condition Comments Blood Detected and Quantified 55.0 (39.0-71.0) uM Adult (>18 years old) Both Normal Not Available Blood Detected and Quantified 93.8 +/- 41.3 uM Adult (>18 years old) Not Specified Normal Not Available Blood Detected and Quantified 90.0 +/- 20.0 uM Newborn (0-30 days old) Not Specified Normal Not Available Blood Detected and Quantified 47.0 +/- 14.0 uM Children (1-13 year old) Female Normal Not Available Blood Detected and Quantified 65.0 +/- 18.0 uM Adult (>18 years old) Male Normal Not Available Blood Detected and Quantified 54.0 +/- 18.0 uM Adult (>18 years old) Female Normal Not Available Blood Detected and Quantified 109.0 +/- 32.0 uM Adult (>18 years old) Both Normal Not Available Blood Detected and Quantified 34.3 +/- 13.0 uM Children (1-13 year old) Both Normal Not Available Blood Detected and Quantified 66.9 +/- 15.3 uM Adult (>18 years old) Not Specified Normal Not Available Cerebrospinal Fluid (CSF) Detected and Quantified 4.87 (3.48-6.26) uM Adult (>18 years old) Both Normal Not Available Cerebrospinal Fluid (CSF) Detected and Quantified 8.3 +/- 4.7 uM Adult (>18 years old) Not Specified Normal Not Available Cerebrospinal Fluid (CSF) Detected and Quantified 6.0 +/- 1.5 uM Adult (>18 years old) Not Specified Normal Not Available Cerebrospinal Fluid (CSF) Detected and Quantified 4.9 +/- 1.6 uM Adult (>18 years old) Not Specified Normal Not Available Cerebrospinal Fluid (CSF) Detected and Quantified 3.7 +/- 1.0 uM Adult (>18 years old) Both Normal Not Available Cerebrospinal Fluid (CSF) Detected and Quantified 4.5 +/- 2.2 uM Adult (>18 years old) Not Specified Normal Not Available Saliva Detected and Quantified >10 uM Adult (>18 years old) Both Normal Not Available Urine Detected and Quantified 5.3 (2.0-8.8) umol/mmol creatinine Adult (>18 years old) Both Normal by GC-MS Urine Detected and Quantified 0.98 umol/mmol creatinine Adult (>18 years old) Both Normal Not Available Urine Detected and not Quantified Not Applicable Adult (>18 years old) Both Normal Not Available Urine Detected and Quantified 2.19 +/- 3.21 umol/mmol creatinine Infant (0-1 year old) Both Normal Not Available Urine Detected and Quantified 2.0 (0.90-2.94) umol/mmol creatinine Adult (>18 years old) Male Normal Not Available Urine Detected and not Quantified Not Applicable Adult (>18 years old) Both Normal Urine compound detected by GC-MS Urine Detected and Quantified 0.0024 - 0.0111 umol/mmol creatinine Adult (>18 years old) Both Normal Not Available Urine Detected and Quantified 0.987 (0.132-1.842) umol/mmol creatinine Adult (>18 years old) Both Normal Not Available Urine Detected and Quantified 4.11 +/- 1.37 umol/mmol creatinine Adult (>18 years old) Both Normal Not Available Urine Detected and Quantified 4.4 (1.2-22.1) umol/mmol creatinine Adult (>18 years old) Both Normal by LC-MS/MS (Biocrates kit) Urine Detected and Quantified 0.050 (0.0-0.098) umol/mmol creatinine Newborn (0-30 days old) Both Normal Not Available Urine Detected and Quantified 0.78 +/- 0.36 umol/mmol creatinine Children (1-13 year old) Male Normal Not Available Urine Detected and Quantified 3.1 +/- 1.46 umol/mmol creatinine Adult (>18 years old) Male Normal Not Available Urine Detected and Quantified 2.6 +/- 1.30 umol/mmol creatinine Adult (>18 years old) Female Normal Not Available Urine Detected and Quantified 0.9 umol/mmol creatinine Adult (>18 years old) Both Normal Not Available
Abnormal Concentrations
	Biofluid Status Value Age Sex Condition Comments Blood Detected and Quantified 65.4 +/- 30.4 uM Adult (>18 years old) Not Specified Heart Transplant Not Available Blood Detected and Quantified 41.0 +/- 16.0 uM Adult (>18 years old) Both Ornithine transcarbamylase (OTC) deficiency Not Available Blood Detected and Quantified 37.8 +/- 12.0 uM Children (1-13 year old) Both Uremia Not Available Blood Detected and Quantified 68.35 +/- 22.43 uM Adult (>18 years old) Both Alzheimer's disease Not Available Cerebrospinal Fluid (CSF) Detected and Quantified 7.6 +/- 3.1 uM Children (1-13 year old) Not Specified Leukemia Not Available Cerebrospinal Fluid (CSF) Detected and Quantified 6.9 +/- 3.6 uM Children (1-13 year old) Not Specified Leukemia Acute Lymphoblastic Leukemia (ALL) with Central... Urine Detected and Quantified 5.0 (2.0-8.0) umol/mmol creatinine Adult (>18 years old) Both Cystinuria Not Available Urine Detected and Quantified 350.0 (200.0-500.0) umol/mmol creatinine Adult (>18 years old) Both Cystinuria Not Available Urine Detected and Quantified 0.0025 - 0.0204 umol/mmol creatinine Adult (>18 years old) Both ADPKD Not Available Urine Detected and Quantified 12.34 +/- 5.07 umol/mmol creatinine Adult (>18 years old) Both Alzheimer's disease Not Available Urine Detected and Quantified 5.00 (2.00-8.00) umol/mmol creatinine Adult (>18 years old) Both Hyperdibasic aminoaciduria I Not Available Urine Detected and Quantified 1285.00 (70.00-2500.00) umol/mmol creatinine Adult (>18 years old) Both Hyperdibasic aminoaciduria I Not Available Urine Detected and Quantified 60.00 (20.00-100.00) umol/mmol creatinine Adult (>18 years old) Both Lysinuric protein intolerance Not Available
Associated Disorders and Diseases
Disease References	Leukemia Peng CT, Wu KH, Lan SJ, Tsai JJ, Tsai FJ, Tsai CH: Amino acid concentrations in cerebrospinal fluid in children with acute lymphoblastic leukemia undergoing chemotherapy. Eur J Cancer. 2005 May;41(8):1158-63. Epub 2005 Apr 14. Pubmed: 15911239 Alzheimer's disease Fonteh AN, Harrington RJ, Tsai A, Liao P, Harrington MG: Free amino acid and dipeptide changes in the body fluids from Alzheimer's disease subjects. Amino Acids. 2007 Feb;32(2):213-24. Epub 2006 Oct 10. Pubmed: 17031479 Uremia Canepa A, Filho JC, Gutierrez A, Carrea A, Forsberg AM, Nilsson E, Verrina E, Perfumo F, Bergstrom J: Free amino acids in plasma, red blood cells, polymorphonuclear leukocytes, and muscle in normal and uraemic children. Nephrol Dial Transplant. 2002 Mar;17(3):413-21. Pubmed: 11865086 Ornithine transcarbamylase deficiency Harada E, Nishiyori A, Tokunaga Y, Watanabe Y, Kuriya N, Kumashiro R, Kuno T, Kuromaru R, Hirose S, Ichikawa K, Yoshino M: Late-onset ornithine transcarbamylase deficiency in male patients: prognostic factors and characteristics of plasma amino acid profile. Pediatr Int. 2006 Apr;48(2):105-11. Pubmed: 16635166 Cystinuria http://www.metagene.de/program/d.prg?mp=CYSTINURIA Hyperdibasic aminoaciduria I http://www.metagene.de/program/d.prg?mp=HYPERDIBASIC%20AMINOACIDURIA%20I Lysinuric protein intolerance http://www.metagene.de/program/d.prg?mp=LYSINURIC%20PROTEIN%20INTOLERANCE%20(LPI)
Associated OMIM IDs	104300 (Alzheimer's disease) 220100 (Cystinuria) 222700 (Lysinuric protein intolerance) 311250 (Ornithine transcarbamylase deficiency) 222690 (Hyperdibasic aminoaciduria I)
External Links
DrugBank ID	DB00129
Phenol Explorer Compound ID	Not Available
Phenol Explorer Metabolite ID	Not Available
FoodDB ID	FDB003654
KNApSAcK ID	Not Available
Chemspider ID	6026
KEGG Compound ID	C00077
BioCyc ID	L-ORNITHINE
BiGG ID	37976
Wikipedia Link	Ornithine
NuGOwiki Link	HMDB00214
Metagene Link	HMDB00214
METLIN ID	27
PubChem Compound	6262
PDB ID	ORN
ChEBI ID	15729
References
Synthesis Reference	Zhang, Peng; Zhang, Shurong; Liu, Chunqiao; Yang, Yuhong. Method for preparing L-ornithine by enzymatic conversion. Faming Zhuanli Shenqing Gongkai Shuomingshu (2007), 8pp.
Material Safety Data Sheet (MSDS)	Download (PDF)
General References	Mayer UM: [Hyperornithinaemia in patients with retinal dystrophy] Ophthalmologe. 2003 Jan;100(1):55-61. Pubmed: 12557027 Peng CT, Wu KH, Lan SJ, Tsai JJ, Tsai FJ, Tsai CH: Amino acid concentrations in cerebrospinal fluid in children with acute lymphoblastic leukemia undergoing chemotherapy. Eur J Cancer. 2005 May;41(8):1158-63. Epub 2005 Apr 14. Pubmed: 15911239 Cynober LA: Plasma amino acid levels with a note on membrane transport: characteristics, regulation, and metabolic significance. Nutrition. 2002 Sep;18(9):761-6. Pubmed: 12297216 Gray RG, Green A, Hall S, McKeown C: Prenatal exclusion of the HHH syndrome. Prenat Diagn. 1995 May;15(5):474-6. Pubmed: 7644438 Peters T, Thaete C, Wolf S, Popp A, Sedlmeier R, Grosse J, Nehls MC, Russ A, Schlueter V: A mouse model for cystinuria type I. Hum Mol Genet. 2003 Sep 1;12(17):2109-20. Pubmed: 12923163 Silwood CJ, Lynch E, Claxson AW, Grootveld MC: 1H and (13)C NMR spectroscopic analysis of human saliva. J Dent Res. 2002 Jun;81(6):422-7. Pubmed: 12097436 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: 9414260 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: 16037230 Nicholson JK, O'Flynn MP, Sadler PJ, Macleod AF, Juul SM, Sonksen PH: Proton-nuclear-magnetic-resonance studies of serum, plasma and urine from fasting normal and diabetic subjects. Biochem J. 1984 Jan 15;217(2):365-75. Pubmed: 6696735 Stadler S, Gempel K, Bieger I, Pontz BF, Gerbitz KD, Bauer MF, Hofmann S: Detection of neonatal argininosuccinate lyase deficiency by serum tandem mass spectrometry. J Inherit Metab Dis. 2001 Jun;24(3):370-8. Pubmed: 11486903 Engelborghs S, Marescau B, De Deyn PP: Amino acids and biogenic amines in cerebrospinal fluid of patients with Parkinson's disease. Neurochem Res. 2003 Aug;28(8):1145-50. Pubmed: 12834252 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: 11329531 Hagenfeldt L, Bjerkenstedt L, Edman G, Sedvall G, Wiesel FA: Amino acids in plasma and CSF and monoamine metabolites in CSF: interrelationship in healthy subjects. J Neurochem. 1984 Mar;42(3):833-7. Pubmed: 6198473 Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. Pubmed: 19212411

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Enzymes
Name: Arginase-1 Reactions: L-arginine + H2O = L-ornithine + urea [RN:R00551] Gene Name: ARG1 Uniprot ID: P05089 Protein Sequence: FASTA Gene Sequence: FASTA
Name: Ornithine aminotransferase, mitochondrial Reactions: L-ornithine + a 2-oxo acid = L-glutamate 5-semialdehyde + an L-amino acid [RN:R01343] Gene Name: OAT Uniprot ID: P04181 Protein Sequence: FASTA Gene Sequence: FASTA
Name: Glycine amidinotransferase, mitochondrial Reactions: L-arginine + glycine = L-ornithine + guanidinoacetate [RN:R00565] Gene Name: GATM Uniprot ID: P50440 Protein Sequence: FASTA Gene Sequence: FASTA
Name: Aminoacylase-1 Reactions: an N-acyl-L-amino acid + H2O = a carboxylate + an L-amino acid [RN:R01263] Gene Name: ACY1 Uniprot ID: Q03154 Protein Sequence: FASTA Gene Sequence: FASTA
Name: Delta-1-pyrroline-5-carboxylate synthase Reactions: ATP + L-glutamate = ADP + L-glutamate 5-phosphate [RN:R00239] Gene Name: ALDH18A1 Uniprot ID: P54886 Protein Sequence: FASTA Gene Sequence: FASTA
Name: Ornithine carbamoyltransferase, mitochondrial Reactions: carbamoyl phosphate + L-ornithine = phosphate + L-citrulline [RN:R01398] Gene Name: OTC Uniprot ID: P00480 Protein Sequence: FASTA Gene Sequence: FASTA
Name: Ornithine decarboxylase Reactions: L-ornithine = putrescine + CO2 [RN:R00670] Gene Name: ODC1 Uniprot ID: P11926 Protein Sequence: FASTA Gene Sequence: FASTA
Name: Arginase-2, mitochondrial Reactions: L-arginine + H2O = L-ornithine + urea [RN:R00551] Gene Name: ARG2 Uniprot ID: P78540 Protein Sequence: FASTA Gene Sequence: FASTA
Name: Cationic amino acid transporter 4 Reactions: Gene Name: SLC7A4 Uniprot ID: O43246 Protein Sequence: FASTA Gene Sequence: FASTA
Name: Mitochondrial ornithine transporter 1 Reactions: --- [] Gene Name: SLC25A15 Uniprot ID: Q9Y619 Protein Sequence: FASTA Gene Sequence: FASTA
Name: Mitochondrial ornithine transporter 2 Reactions: Gene Name: SLC25A2 Uniprot ID: Q9BXI2 Protein Sequence: FASTA Gene Sequence: FASTA
Name: Cationic amino acid transporter 3 Reactions: --- [] Gene Name: SLC7A3 Uniprot ID: Q8WY07 Protein Sequence: FASTA Gene Sequence: FASTA
Name: High affinity cationic amino acid transporter 1 Reactions: --- [] Gene Name: SLC7A1 Uniprot ID: P30825 Protein Sequence: FASTA Gene Sequence: FASTA
Name: Low affinity cationic amino acid transporter 2 Reactions: Gene Name: SLC7A2 Uniprot ID: P52569 Protein Sequence: FASTA Gene Sequence: FASTA
Name: Y+L amino acid transporter 2 Reactions: Gene Name: SLC7A6 Uniprot ID: Q92536 Protein Sequence: FASTA Gene Sequence: FASTA
Name: Ornithine decarboxylase antizyme 1 Reactions: Gene Name: OAZ1 Uniprot ID: P54368 Protein Sequence: FASTA Gene Sequence: FASTA
Name: Ornithine decarboxylase antizyme 2 Reactions: Gene Name: OAZ2 Uniprot ID: O95190 Protein Sequence: FASTA Gene Sequence: FASTA
Name: Ornithine decarboxylase antizyme 3 Reactions: Gene Name: OAZ3 Uniprot ID: Q9UMX2 Protein Sequence: FASTA Gene Sequence: FASTA
Name: Antizyme inhibitor 1 Reactions: Gene Name: AZIN1 Uniprot ID: O14977 Protein Sequence: FASTA Gene Sequence: FASTA

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