Ornithine (YMDB00353)

You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.

Identification

YMDB ID

YMDB00353

Name

Ornithine

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Ornithine, 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

MOL SDF PDB SMILES InChI

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 number

70-26-8

Weight

Average: 132.161
Monoisotopic: 132.089877638

InChI Key

AHLPHDHHMVZTML-BYPYZUCNSA-N

InChI

InChI=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 Name

ornithine

Chemical Formula

C₅H₁₂N₂O₂

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.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-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 Framework

Aliphatic acyclic compounds

External Descriptors

non-proteinogenic L-alpha-amino acid (CHEBI:15729 )
ornithine (CHEBI:15729 )
Other amino acids (C00077 )

Physical Properties

State

Solid

Charge

Melting point

140 °C

Experimental Properties

Property	Value	Reference
Water Solubility	620 mg/mL [HMP experimental]	PhysProp
LogP	-4.22 [SANGSTER (1994)]	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	172 g/L	ALOGPS
logP	-3.6	ALOGPS
logP	-3.7	ChemAxon
logS	0.11	ALOGPS
pKa (Strongest Acidic)	2.67	ChemAxon
pKa (Strongest Basic)	10.29	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	89.34 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	33.21 m³·mol⁻¹	ChemAxon
Polarizability	13.85 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

Cytoplasm, Extracellular, Mitochondrion

Organoleptic Properties

Not Available

SMPDB Pathways

Glutamate Metabolism	PW002376
beta-Alanine metabolism	PW002381

KEGG Pathways

beta-Alanine metabolism

ec00410

SMPDB Reactions

L-Arginine + water → Ornithine + Urea

Ornithine + Oxoglutaric acid ↔ L-Glutamic acid + l-Glutamic-gamma-semialdehyde

Ornithine + hydron → Carbon dioxide + Putrescine

KEGG Reactions

Concentrations

Intracellular Concentrations

Intracellular Concentration	Substrate	Growth Conditions	Strain	Citation
132 ± 7 µM	YEB media with 0.5 mM glucose	aerobic	Baker's yeast	Experimentally Determined Not Available
7000 ± 0 µM	Minimal medium supplemented with ammonium and glucose	aerobic;growing cells	Baker's yeast	PMID: 4578278
20000 ± 0 µM	Minimal medium supplemented with arginine and glucose	aerobic;growing cells	Baker's yeast	PMID: 4578278
330000 ± 0 µM	Minimal medium supplemented with ornithine and glucose	aerobic;growing cells	Baker's yeast	PMID: 4578278
22000 ± 0 µM	Minimal medium supplemented with citrulline and glucose	aerobic;growing cells	Baker's yeast	PMID: 4578278
Conversion Details Here

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (2 TMS)	splash10-0006-1920000000-b0357b8c9888abda7d80	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-0006-0910000000-8aaa0faabf1429b90611	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (2 TMS)	splash10-00di-7910000000-5fa118444ceb45204aa3	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-006x-3910000000-f6d0c6492f2cab33a392	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-00dr-2900000000-77222ff2d0118d3d3b57	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (4 TMS)	splash10-0006-1910000000-53c73c4fa3665c44d3b9	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (5 TMS)	splash10-03di-1691000000-dc14976cfee86cc828b9	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-0006-0920000000-f65f61e4a3739eabb1d1	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0006-1920000000-b0357b8c9888abda7d80	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0006-0910000000-8aaa0faabf1429b90611	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-7910000000-5fa118444ceb45204aa3	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-006x-3910000000-f6d0c6492f2cab33a392	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-00dr-2900000000-77222ff2d0118d3d3b57	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0006-1910000000-53c73c4fa3665c44d3b9	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-03di-1691000000-dc14976cfee86cc828b9	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0006-0900000000-f59681b9f46f1b738487	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0006-0900000000-3048477975b51ae176af	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00dr-2900000000-8d1a2cc0a88f7d9216e1	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0udi-1900000000-bc40b76e8b03ef7a08f0	JSpectraViewer \| MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-001l-9000000000-50fe14c2cb68fd09e32f	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-0089-9300000000-bbfdea03043e52ad8a15	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-000i-0793321000-9fef988b5ce019f84642	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-03di-0900000000-a612df8df5f8ba1ff7f3	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-001i-0910000000-97fad20414656e2b7b93	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-01di-0490000000-1b137b937beb110d2e4b	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-001i-0900000000-e3fc95eb909e45d8e648	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-001i-1900000000-cdd9aac89a5a71814ff3	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-001r-9500000000-f1cc3eccf3f5ab734222	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-001i-0900000000-e3fc95eb909e45d8e648	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-001i-1900000000-cdd9aac89a5a71814ff3	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-001r-9500000000-f1cc3eccf3f5ab734222	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , negative	splash10-03di-0900000000-a612df8df5f8ba1ff7f3	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , negative	splash10-001i-0910000000-97fad20414656e2b7b93	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , negative	splash10-01di-0490000000-1b137b937beb110d2e4b	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0159-9600000000-d6a4da521a68d6118935	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-001i-5900000000-9ba2d098f91a6c2aa867	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-001i-0900000000-420c81f823f109c194eb	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-00kb-9000000000-f91c664b0ccbf52d8c69	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-001i-0900000000-10da18da37a65c3afb75	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-01b9-6900000000-8fe592b77d2d8e4ae704	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-00di-9000000000-462b84db532c33527580	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-00di-9000000000-9c9c28d2e40d5eadacd2	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-001i-0900000000-e44e06092c06bb4791af	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-014i-9000000000-4d6ccc429f5155b24654	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-014i-0900000000-dcad699e8ed7e1b19860	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-001i-0900000000-7b130437d4e1ceea277b	JSpectraViewer \| MoNA
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
2D NMR	[1H,1H] 2D NMR Spectrum	Not Available	JSpectraViewer
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	JSpectraViewer

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:

Resource	Link
CHEBI ID	15729
HMDB ID	HMDB00214
Pubchem Compound ID	6262
Kegg ID	C01602
ChemSpider ID	6026
FOODB ID	FDB030969
Wikipedia	Ornithine
BioCyc ID	L-ORNITHINE

Enzymes

Protein Details

1. Arginase

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.

Protein Details

2. Arginine biosynthesis bifunctional protein ArgJ, mitochondrial

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.

Protein Details

3. Ornithine carbamoyltransferase

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.

Protein Details

4. Ornithine decarboxylase

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).

Protein Details

5. Ornithine aminotransferase

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.

Structure for #<Compound:0xa68938c4>

Enzymes

Reactions

Reactions

Reactions

Reactions

Reactions