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Identification
YMDB IDYMDB00353
NameOrnithine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionOrnithine, also known as (S)-ornithine, belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom. Ornithine is a very strong basic compound (based on its pKa). Ornithine exists in all living species, ranging from bacteria to humans. Ornithine is a potentially toxic compound.
Structure
Thumb
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
  • (S)-2,5-Diaminovaleric acid
  • (S)-alpha,delta-Diaminovaleric acid
  • (S)-2,5-Diaminovalerate
  • (S)-a,delta-Diaminovalerate
  • (S)-a,delta-Diaminovaleric acid
  • (S)-alpha,delta-Diaminovalerate
  • (S)-Α,δ-diaminovalerate
  • (S)-Α,δ-diaminovaleric acid
  • (S)-a,Δ-diaminovalerate
  • (S)-a,Δ-diaminovaleric acid
  • 2,5-Diaminopentanoic acid
  • Ornithine dihydrochloride, (L)-isomer
  • Ornithine hydrochloride, (D)-isomer
  • Ornithine, (D)-isomer
  • Ornithine, (L)-isomer
  • 2,5 Diaminopentanoic acid
  • Ornithine monoacetate, (L)-isomer
  • Ornithine monohydrochloride, (D)-isomer
  • Ornithine monohydrochloride, (DL)-isomer
  • Ornithine phosphate (1:1), (L)-isomer
  • Ornithine sulfate (1:1), (L)-isomer
  • Ornithine hydrochloride, (DL)-isomer
  • Ornithine hydrochloride, (L)-isomer
  • Ornithine monohydrobromide, (L)-isomer
  • Ornithine, (DL)-isomer
CAS number70-26-8
WeightAverage: 132.161
Monoisotopic: 132.089877638
InChI KeyAHLPHDHHMVZTML-BYPYZUCNSA-N
InChIInChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1
IUPAC Name(2S)-2,5-diaminopentanoic acid
Traditional IUPAC Nameornithine
Chemical FormulaC5H12N2O2
SMILES[H]OC(=O)[C@@]([H])(N([H])[H])C([H])([H])C([H])([H])C([H])([H])N([H])[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentL-alpha-amino acids
Alternative Parents
Substituents
  • L-alpha-amino acid
  • Fatty acid
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Amine
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Primary aliphatic amine
  • Organic nitrogen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting point140 °C
Experimental Properties
PropertyValueReference
Water Solubility620 mg/mL [HMP experimental]PhysProp
LogP-4.22 [SANGSTER (1994)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility172 g/LALOGPS
logP-3.6ALOGPS
logP-3.7ChemAxon
logS0.11ALOGPS
pKa (Strongest Acidic)2.67ChemAxon
pKa (Strongest Basic)10.29ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area89.34 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity33.21 m³·mol⁻¹ChemAxon
Polarizability13.85 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • Cytoplasm, Extracellular, Mitochondrion
Organoleptic PropertiesNot Available
SMPDB Pathways
Glutamate MetabolismPW002376 ThumbThumb?image type=greyscaleThumb?image type=simple
beta-Alanine metabolismPW002381 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
beta-Alanine metabolismec00410 Map00410
SMPDB Reactions
L-Arginine + waterOrnithine + Urea
Ornithine + Oxoglutaric acidL-Glutamic acid + l-Glutamic-gamma-semialdehyde
Ornithine + hydronCarbon dioxide + Putrescine
KEGG Reactions
L-Arginine + waterOrnithine + Urea
Ornithine + CarbamoylphosphateCitrulline + phosphate + hydron
Ornithine + hydronPutrescine + Carbon dioxide
L-Glutamic acid + N-AcetylornithineN-acetyl-L-glutamic acid + Ornithine
Oxoglutaric acid + OrnithineL-Glutamic acid + l-Glutamic-gamma-semialdehyde
Concentrations
Intracellular Concentrations
Intracellular ConcentrationSubstrateGrowth ConditionsStrainCitation
132 ± 7 µM YEB media with 0.5 mM glucoseaerobicBaker's yeastExperimentally Determined
Not Available
7000 ± 0 µM Minimal medium supplemented with ammonium and glucoseaerobic;growing cellsBaker's yeastPMID: 4578278
20000 ± 0 µM Minimal medium supplemented with arginine and glucoseaerobic;growing cellsBaker's yeastPMID: 4578278
330000 ± 0 µM Minimal medium supplemented with ornithine and glucoseaerobic;growing cellsBaker's yeastPMID: 4578278
22000 ± 0 µM Minimal medium supplemented with citrulline and glucoseaerobic;growing cellsBaker's yeastPMID: 4578278
Conversion Details Here
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (2 TMS)splash10-0006-1920000000-b0357b8c9888abda7d80JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-0006-0910000000-8aaa0faabf1429b90611JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (2 TMS)splash10-00di-7910000000-5fa118444ceb45204aa3JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-006x-3910000000-f6d0c6492f2cab33a392JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-00dr-2900000000-77222ff2d0118d3d3b57JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (4 TMS)splash10-0006-1910000000-53c73c4fa3665c44d3b9JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (5 TMS)splash10-03di-1691000000-dc14976cfee86cc828b9JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-0006-0920000000-f65f61e4a3739eabb1d1JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0006-1920000000-b0357b8c9888abda7d80JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0006-0910000000-8aaa0faabf1429b90611JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00di-7910000000-5fa118444ceb45204aa3JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-006x-3910000000-f6d0c6492f2cab33a392JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-00dr-2900000000-77222ff2d0118d3d3b57JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0006-1910000000-53c73c4fa3665c44d3b9JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-03di-1691000000-dc14976cfee86cc828b9JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0006-0900000000-f59681b9f46f1b738487JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0006-0900000000-3048477975b51ae176afJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00dr-2900000000-8d1a2cc0a88f7d9216e1JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-1900000000-bc40b76e8b03ef7a08f0JSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-001l-9000000000-50fe14c2cb68fd09e32fJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-0089-9300000000-bbfdea03043e52ad8a15JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-000i-0793321000-9fef988b5ce019f84642JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-03di-0900000000-a612df8df5f8ba1ff7f3JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-001i-0910000000-97fad20414656e2b7b93JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-01di-0490000000-1b137b937beb110d2e4bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-001i-0900000000-e3fc95eb909e45d8e648JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-001i-1900000000-cdd9aac89a5a71814ff3JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-001r-9500000000-f1cc3eccf3f5ab734222JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-001i-0900000000-e3fc95eb909e45d8e648JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-001i-1900000000-cdd9aac89a5a71814ff3JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-001r-9500000000-f1cc3eccf3f5ab734222JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-03di-0900000000-a612df8df5f8ba1ff7f3JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-001i-0910000000-97fad20414656e2b7b93JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-01di-0490000000-1b137b937beb110d2e4bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0159-9600000000-d6a4da521a68d6118935JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-001i-5900000000-9ba2d098f91a6c2aa867JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-001i-0900000000-420c81f823f109c194ebJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-00kb-9000000000-f91c664b0ccbf52d8c69JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-001i-0900000000-10da18da37a65c3afb75JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-01b9-6900000000-8fe592b77d2d8e4ae704JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-00di-9000000000-462b84db532c33527580JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-00di-9000000000-9c9c28d2e40d5eadacd2JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-001i-0900000000-e44e06092c06bb4791afJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-014i-9000000000-4d6ccc429f5155b24654JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-014i-0900000000-dcad699e8ed7e1b19860JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-001i-0900000000-7b130437d4e1ceea277bJSpectraViewer | MoNA
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Abadjieva, A., Pauwels, K., Hilven, P., Crabeel, M. (2001). "A new yeast metabolon involving at least the two first enzymes of arginine biosynthesis: acetylglutamate synthase activity requires complex formation with acetylglutamate kinase." J Biol Chem 276:42869-42880.11553611
  • Eisenstein, E., Osborne, J. C. Jr, Chaiken, I. M., Hensley, P. (1984). "Purification and characterization of ornithine transcarbamoylase from Saccharomyces cerevisiae." J Biol Chem 259:5139-5145.6370999
  • Pirkov, I., Norbeck, J., Gustafsson, L., Albers, E. (2008). "A complete inventory of all enzymes in the eukaryotic methionine salvage pathway." FEBS J 275:4111-4120.18625006
  • Gancedo, J. M., Gancedo, C. (1973). "Concentrations of intermediary metabolites in yeast." Biochimie 55:205-211.4578278
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.
External Links:
ResourceLink
CHEBI ID15729
HMDB IDHMDB00214
Pubchem Compound ID6262
Kegg IDC01602
ChemSpider ID6026
FOODB IDFDB030969
WikipediaOrnithine
BioCyc IDL-ORNITHINE

Enzymes

General function:
Involved in arginase activity
Specific function:
L-arginine + H(2)O = L-ornithine + urea
Gene Name:
CAR1
Uniprot ID:
P00812
Molecular weight:
35661.60156
Reactions
L-arginine + H(2)O → L-ornithine + urea.
General function:
Involved in glutamate N-acetyltransferase activity
Specific function:
Catalyzes two activities which are involved in the cyclic version of arginine biosynthesis:the synthesis of acetylglutamate from glutamate and acetyl-CoA, and of ornithine by transacetylation between acetylornithine and glutamate
Gene Name:
ARG7
Uniprot ID:
Q04728
Molecular weight:
47848.30078
Reactions
N(2)-acetyl-L-ornithine + L-glutamate → L-ornithine + N-acetyl-L-glutamate.
Acetyl-CoA + L-glutamate → CoA + N-acetyl-L-glutamate.
General function:
Involved in carboxyl- or carbamoyltransferase activity
Specific function:
Carbamoyl phosphate + L-ornithine = phosphate + L-citrulline
Gene Name:
ARG3
Uniprot ID:
P05150
Molecular weight:
37844.80078
Reactions
Carbamoyl phosphate + L-ornithine → phosphate + L-citrulline.
General function:
Involved in catalytic activity
Specific function:
L-ornithine = putrescine + CO(2)
Gene Name:
SPE1
Uniprot ID:
P08432
Molecular weight:
52284.80078
Reactions
L-ornithine → putrescine + CO(2).
General function:
Involved in transaminase activity
Specific function:
L-ornithine + a 2-oxo acid = L-glutamate 5- semialdehyde + an L-amino acid
Gene Name:
CAR2
Uniprot ID:
P07991
Molecular weight:
46085.60156
Reactions
L-ornithine + a 2-oxo acid → L-glutamate 5-semialdehyde + an L-amino acid.