L-Cystathionine (YMDB00245)

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Identification

YMDB ID

YMDB00245

Name

L-Cystathionine

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

L-Cystathionine belongs to the class of organic compounds known as l-cysteine-s-conjugates. L-cysteine-S-conjugates are compounds containing L-cysteine where the thio-group is conjugated. L-Cystathionine is a very strong basic compound (based on its pKa). L-Cystathionine exists in all living species, ranging from bacteria to humans. Within yeast, L-cystathionine participates in a number of enzymatic reactions. In particular, L-cystathionine can be biosynthesized from homocysteine and L-serine through its interaction with the enzyme cystathionine beta-synthase. In addition, L-cystathionine can be converted into ammonium, L-cysteine, and 2-ketobutyric acid; which is catalyzed by the enzyme cystathionine gamma-lyase. In yeast, L-cystathionine is involved in the metabolic pathway called the sulfur metabolism pathway. L-Cystathionine is a potentially toxic compound.

Structure

MOL SDF PDB SMILES InChI

Synonyms

(R)-S-(2-amino-2-carboxyethyl)-L-Homocysteine
[R-(R*,S*)]-2-amino-4-[(2-amino-2-carboxyethyl)thio]-Butanoate
[R-(R*,S*)]-2-amino-4-[(2-amino-2-carboxyethyl)thio]-Butanoic acid
Cystathionine
L-(+)-Cystathionine
S-[(2R)-2-amino-2-carboxyethyl]-L-Homocysteine
S-(beta-Amino-beta-carboxyethyl)homocysteine
S-(b-Amino-b-carboxyethyl)homocysteine
S-(Β-amino-β-carboxyethyl)homocysteine

CAS number

56-88-2

Weight

Average: 222.262
Monoisotopic: 222.067427636

InChI Key

ILRYLPWNYFXEMH-WHFBIAKZSA-N

InChI

InChI=1S/C7H14N2O4S/c8-4(6(10)11)1-2-14-3-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)/t4-,5-/m0/s1

IUPAC Name

(2S)-2-amino-4-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}butanoic acid

Traditional IUPAC Name

L-cystathionine

Chemical Formula

C₇H₁₄N₂O₄S

SMILES

[H]OC(=O)[C@@]([H])(N([H])[H])C([H])([H])SC([H])([H])C([H])([H])[C@]([H])(N([H])[H])C(=O)O[H]

Chemical Taxonomy

Description

belongs to the class of organic compounds known as l-cysteine-s-conjugates. L-cysteine-S-conjugates are compounds containing L-cysteine where the thio-group is conjugated.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-cysteine-S-conjugates

Alternative Parents

Substituents

L-cysteine-s-conjugate
Alpha-amino acid
L-alpha-amino acid
Thia fatty acid
Dicarboxylic acid or derivatives
Fatty acyl
Fatty acid
Amino acid
Carboxylic acid
Thioether
Dialkylthioether
Sulfenyl compound
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Primary amine
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Organopnictogen compound
Organic oxygen compound
Carbonyl group
Amine
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

cystathionine (CHEBI:17482 )

Physical Properties

State

Solid

Charge

Melting point

312 °C

Experimental Properties

Property	Value	Reference
Water Solubility	22 mg/mL [HMP experimental]	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	17.3 g/L	ALOGPS
logP	-4	ALOGPS
logP	-5.8	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	1.79	ChemAxon
pKa (Strongest Basic)	9.66	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	126.64 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	51.57 m³·mol⁻¹	ChemAxon
Polarizability	22.02 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

Organoleptic Properties

Not Available

SMPDB Pathways

Cysteine Metabolism	PW002383
Sulfur metabolism	PW002483

KEGG Pathways

Cysteine and methionine metabolism	ec00270
Glycine, serine and threonine metabolism	ec00260
Sulfur metabolism	ec00920

SMPDB Reactions

Homocysteine + Pyruvic acid + Ammonium → water + L-Cystathionine

Homocysteine + L-Serine → water + L-Cystathionine

water + L-Cystathionine → Ammonium + L-Cysteine + 2-Ketobutyric acid

KEGG Reactions

L-Cystathionine + water → L-Homocysteine + Pyruvic acid + Ammonium

L-Homocysteine + L-Serine → L-Cystathionine + water

L-Cystathionine + water → L-Cysteine + Ammonium + 2-Ketobutyric acid

L-Cysteine + O-Acetyl-L-homoserine → Acetic acid + L-Cystathionine + hydron

O-Succinyl-L-homoserine + L-Cysteine → L-Cystathionine + hydron + Succinic acid

Concentrations

Intracellular Concentrations

Not Available

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) (4 TMS)	splash10-00fr-8950000000-640b4294e37e5a01048d	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (2 TMS)	splash10-0f7c-7910000000-91f9f2b2dd44a3cdb276	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-00or-1940000000-c0d688e4ea87ff3e03fa	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (4 TMS)	splash10-00or-0980000000-7d816de782a902900d0e	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00fr-8950000000-640b4294e37e5a01048d	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0f7c-7910000000-91f9f2b2dd44a3cdb276	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-00or-1940000000-c0d688e4ea87ff3e03fa	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-00or-0980000000-7d816de782a902900d0e	JSpectraViewer \| MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-00di-9410000000-9487e9168e86a2297931	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-00dm-9665000000-608a6335880ad1c2519d	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_1) - 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
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0089-1980000000-99cb7d1da067e5436b09	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-000i-9200000000-fb776970b6ef36e72725	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-000i-9200000000-fb776970b6ef36e72725	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-00fr-0690000000-0b572de3fcbc7e2f13cc	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-000t-0900000000-5788192b32aadd177e33	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-000b-4900000000-b86ac7de446a762365bd	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-000j-9800000000-75ff1bc6e325692a9da9	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-00kr-9100000000-6517562dc0f31a85afc8	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive	splash10-001i-0900000000-d1628d0a880f1b6e6d90	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive	splash10-000i-9000000000-9a2e1e54b77216e2df72	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-00di-0090000000-36678c2f0bf1b01cc9d4	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) 30V, Positive	splash10-05fr-0190000000-e575f57f0d76ef6afa49	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-00e9-0940000000-962ae510f06296b98878	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-00e9-0940000000-27da1912eac54f485bfa	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-00fr-0690000000-82fe2198c98660008c04	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-000t-0900000000-58cceb69cceeff79606c	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-000b-4900000000-5877787c54120dc165c9	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-000j-9800000000-fd29b0fcf62b73831829	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-00kr-9100000000-6517562dc0f31a85afc8	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-05di-1930000000-887e3ad7da04e4f1aac9	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-01uc-6900000000-563444ac8ab717997268	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0uki-9700000000-35397d8e2ab2c6582c52	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-0970000000-d0f0a96ca41d1f751c26	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0089-3910000000-22200c974305822456d8	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-008l-9300000000-0dfaab5efe3438889c3c	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	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C 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
Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
Jhee, K. H., McPhie, P., Miles, E. W. (2000). "Yeast cystathionine beta-synthase is a pyridoxal phosphate enzyme but, unlike the human enzyme, is not a heme protein." J Biol Chem 275:11541-11544.10766767
Castrillo, J. I., Zeef, L. A., Hoyle, D. C., Zhang, N., Hayes, A., Gardner, D. C., Cornell, M. J., Petty, J., Hakes, L., Wardleworth, L., Rash, B., Brown, M., Dunn, W. B., Broadhurst, D., O'Donoghue, K., Hester, S. S., Dunkley, T. P., Hart, S. R., Swainston, N., Li, P., Gaskell, S. J., Paton, N. W., Lilley, K. S., Kell, D. B., Oliver, S. G. (2007). "Growth control of the eukaryote cell: a systems biology study in yeast." J Biol 6:4.17439666

Synthesis Reference:

Yamagata, Shuzo; Akamatsu, Tsuyoshi; Iwama, Tomonori. Immobilization of Saccharomyces cerevisiae cystathionine gamma-lyase and application of the product to cystathionine synthesis. Applied and Environmental Microbiology (2004), 70(6), 3766-3768.

External Links:

Resource	Link
CHEBI ID	17482
HMDB ID	HMDB00099
Pubchem Compound ID	439258
Kegg ID	C02291
ChemSpider ID	388392
FOODB ID	FDB001976
Wikipedia	Cystathionine
BioCyc ID	L-CYSTATHIONINE

Enzymes

Protein Details

1. Putative cystathionine gamma-synthase YML082W

General function:: Involved in pyridoxal phosphate binding
Specific function:: O(4)-succinyl-L-homoserine + L-cysteine = L- cystathionine + succinate
Gene Name:: Not Available
Uniprot ID:: Q04533
Molecular weight:: 74312.70313

Reactions

O(4)-succinyl-L-homoserine + L-cysteine → L-cystathionine + succinate.

Protein Details

2. Cystathionine gamma-lyase

General function:: Involved in pyridoxal phosphate binding
Specific function:: L-cystathionine + H(2)O = L-cysteine + NH(3) + 2-oxobutanoate
Gene Name:: CYS3
Uniprot ID:: P31373
Molecular weight:: 42541.69922

Reactions

L-cystathionine + H(2)O → L-cysteine + NH(3) + 2-oxobutanoate.

Protein Details

3. Putative cystathionine gamma-synthase YLL058W

General function:: Involved in pyridoxal phosphate binding
Specific function:: O(4)-succinyl-L-homoserine + L-cysteine = L- cystathionine + succinate
Gene Name:: Not Available
Uniprot ID:: Q12198
Molecular weight:: 64222.80078

Reactions

O(4)-succinyl-L-homoserine + L-cysteine → L-cystathionine + succinate.

Protein Details

4. Cystathionine gamma-synthase

General function:: Involved in pyridoxal phosphate binding
Specific function:: O(4)-succinyl-L-homoserine + L-cysteine = L- cystathionine + succinate
Gene Name:: STR2
Uniprot ID:: P47164
Molecular weight:: 72349.89844

Reactions

O(4)-succinyl-L-homoserine + L-cysteine → L-cystathionine + succinate.

Protein Details

5. Cystathionine beta-lyase

General function:: Involved in pyridoxal phosphate binding
Specific function:: L-cystathionine + H(2)O = L-homocysteine + NH(3) + pyruvate
Gene Name:: STR3
Uniprot ID:: P53101
Molecular weight:: 51828.0

Reactions

L-cystathionine + H(2)O → L-homocysteine + NH(3) + pyruvate.

Protein Details

6. Putative cystathionine beta-lyase

General function:: Involved in pyridoxal phosphate binding
Specific function:: L-cystathionine + H(2)O = L-homocysteine + NH(3) + pyruvate
Gene Name:: IRC7
Uniprot ID:: P43623
Molecular weight:: 36971.10156

Reactions

L-cystathionine + H(2)O → L-homocysteine + NH(3) + pyruvate.

Protein Details

7. Cystathionine beta-synthase

General function:: Involved in cysteine biosynthetic process from serine
Specific function:: L-serine + L-homocysteine = L-cystathionine + H(2)O
Gene Name:: CYS4
Uniprot ID:: P32582
Molecular weight:: 56021.30078

Reactions

L-serine + L-homocysteine → L-cystathionine + H(2)O.

Structure for #<Compound:0xafc63c34>

Enzymes

Reactions

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