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L-Homocysteine (YMDB00520)

Identification
YMDB IDYMDB00520
NameL-Homocysteine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionHomocysteine, also known as Hcy or homo-cys, 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. Homocysteine is a very strong basic compound (based on its pKa). Homocysteine exists in all living species, ranging from bacteria to humans. Homocysteine is a potentially toxic compound.
Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
  • (S)-2-amino-4-mercapto-butanoic acid
  • 2-amino-4-mercapto-butanoic acid
  • 2-amino-4-mercapto-butyric acid
  • 2-Amino-4-mercaptobutyric acid
  • Hcy
  • Homocysteine
  • l-2-amino-4-mercaptobutyric acid
  • L-homocysteine
  • L-2-Amino-4-mercaptobutyrate
  • Homocysteine, L isomer
  • L-Isomer homocysteine
  • 2 Amino 4 mercaptobutyric acid
  • Homocysteine, L-isomer
  • (S)-2-Amino-4-mercapto-butanoate
  • (S)-2-Amino-4-mercaptobutanoic acid
  • (S)-Homocysteine
  • 2-Amino-4-mercapto-DL-butyrate
  • 2-Amino-4-mercapto-DL-butyric acid
  • 2-Amino-4-mercapto-L-butyric acid
  • 2-Amino-4-mercapto-butanoate
  • 2-Amino-4-mercapto-butyric acid
  • 2-Amino-4-sulfanylbutanoate
  • 2-Amino-4-sulfanylbutanoic acid
  • D,L-Homocysteine
  • DL-2-Amino-4-mercapto-butyric acid
  • DL-2-Amino-4-mercaptobutyric acid
  • DL-Homocysteine
  • Homo-cys
  • L-2-Amino-4-mercapto-butyric acid
  • 2-Amino-4-mercapto-butyrate
CAS number6027-13-0
WeightAverage: 135.185
Monoisotopic: 135.035399227
InChI KeyFFFHZYDWPBMWHY-VKHMYHEASA-N
InChIInChI=1S/C4H9NO2S/c5-3(1-2-8)4(6)7/h3,8H,1-2,5H2,(H,6,7)/t3-/m0/s1
IUPAC Name(2S)-2-amino-4-sulfanylbutanoic acid
Traditional IUPAC NameL-homocysteine
Chemical FormulaC4H9NO2S
SMILESN[C@@H](CCS)C(O)=O
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
  • Thia fatty acid
  • Fatty acid
  • Fatty acyl
  • Amino acid
  • Alkylthiol
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Primary amine
  • Organosulfur compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Primary aliphatic amine
  • Organic oxygen compound
  • Carbonyl group
  • Amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting point232.5 °C
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility14.8 g/LALOGPS
logP-2.3ALOGPS
logP-2.6ChemAxon
logS-0.96ALOGPS
pKa (Strongest Acidic)2.46ChemAxon
pKa (Strongest Basic)9.41ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area63.32 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity32.94 m³·mol⁻¹ChemAxon
Polarizability13.54 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • peroxisome
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Cysteine MetabolismPW002383 ThumbThumb?image type=greyscaleThumb?image type=simple
Methionine metabolism and salvagePW002384 ThumbThumb?image type=greyscaleThumb?image type=simple
One Carbon Pool by Folate IPW002468 ThumbThumb?image type=greyscaleThumb?image type=simple
Sulfur metabolismPW002483 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Cysteine and methionine metabolismec00270 Map00270
Sulfur metabolismec00920 Map00920
SMPDB ReactionsNot Available
KEGG Reactions
L-Homocysteine + 5-Methyltetrahydropteroyltri-L-glutamic acid → L-Methionine + Tetrahydropteroyltri-L-glutamate
S-Adenosylhomocysteine + water → Adenosine + L-Homocysteine
L-Cystathionine + water → L-Homocysteine + Pyruvic acid + Ammonium
L-Homocysteine + L-Serine → L-Cystathionine + water
L-Homocysteine + S-Adenosylmethionine → L-Methionine + S-Adenosylhomocysteine + hydron
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-004i-0920000000-20fbffbe76510c066e6fJSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9000000000-1f800d28bca4b2b7a49fJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_1) - 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
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-014l-4900000000-c50d79ba3a5013bcf29fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-000i-9000000000-025c9e1f4fb58138c43bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-014i-4900000000-33f205e002f49f034764JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-052r-0900000000-c1f98c8182b5ddc09cb1JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00ko-9800000000-80a1c80328e8836233a4JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0006-9100000000-1f611da44349ffdfaefeJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0bvi-9000000000-c9d62a66522e46a17f56JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001i-3900000000-e8322d5858cba16a3bd2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00lr-6900000000-e0190a1cc33e605bac0aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-001i-9000000000-900bb5d8fb11bec02e39JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001i-0900000000-38e427e24202b2411597JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-7900000000-5cf2133d9faac56032d3JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-001i-9000000000-942ac689538269d6ca7bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0006-9000000000-166428542631f9ac0714JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a4i-9000000000-9bcb57b924579a6c3411JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4j-9000000000-8eee886864db64f3eec2JSpectraViewer
1D NMR1H 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 NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • 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
  • 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
  • Mulet, J. M., Alemany, B., Ros, R., Calvete, J. J., Serrano, R. (2004). "Expression of a plant serine O-acetyltransferase in Saccharomyces cerevisiae confers osmotic tolerance and creates an alternative pathway for cysteine biosynthesis." Yeast 21:303-312.15042590
  • 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
  • Suliman, H. S., Sawyer, G. M., Appling, D. R., Robertus, J. D. (2005). "Purification and properties of cobalamin-independent methionine synthase from Candida albicans and Saccharomyces cerevisiae." Arch Biochem Biophys 441:56-63.16083849
  • Thomas, D., Becker, A., Surdin-Kerjan, Y. (2000). "Reverse methionine biosynthesis from S-adenosylmethionine in eukaryotic cells." J Biol Chem 275:40718-40724.11013242
  • Tehlivets, O., Hasslacher, M., Kohlwein, S. D. (2004). "S-adenosyl-L-homocysteine hydrolase in yeast: key enzyme of methylation metabolism and coordinated regulation with phospholipid synthesis." FEBS Lett 577:501-506.15556636
  • Csaikl, U., Csaikl, F. (1986). "Molecular cloning and characterization of the MET6 gene of Saccharomyces cerevisiae." Gene 46:207-214.3542720
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID17588
HMDB IDHMDB0000742
Pubchem Compound ID91552
Kegg IDC00155
ChemSpider ID82666
FOODB IDFDB001491
WikipediaHomocysteine
BioCyc IDHOMO-CYS

Enzymes

Protein Details
1. Protein MET17
General function:
Involved in pyridoxal phosphate binding
Specific function:
Transforms O-acetylhomoserine into homocysteine and O- acetylserine into cysteine
Gene Name:
MET17
Uniprot ID:
P06106
Molecular weight:
48671.39844
Reactions
O-acetyl-L-homoserine + methanethiol → L-methionine + acetate.
O(3)-acetyl-L-serine + H(2)S → L-cysteine + acetate.
Protein Details
2. Adenosylhomocysteinase
General function:
Involved in adenosylhomocysteinase activity
Specific function:
Adenosylhomocysteine is a competitive inhibitor of S- adenosyl-L-methionine-dependent methyl transferase reactions; therefore adenosylhomocysteinase may play a key role in the control of methylations via regulation of the intracellular concentration of adenosylhomocysteine
Gene Name:
SAH1
Uniprot ID:
P39954
Molecular weight:
49125.10156
Reactions
S-adenosyl-L-homocysteine + H(2)O → L-homocysteine + adenosine.
Protein Details
3. 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
General function:
Involved in 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity
Specific function:
Catalyzes the transfer of a methyl group from 5- methyltetrahydrofolate to homocysteine resulting in methionine formation
Gene Name:
MET6
Uniprot ID:
P05694
Molecular weight:
85859.20313
Reactions
5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine → tetrahydropteroyltri-L-glutamate + L-methionine.
Protein Details
4. 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
5. 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
6. 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.
Protein Details
7. Homocysteine S-methyltransferase 1
General function:
Involved in homocysteine S-methyltransferase activity
Specific function:
Homocysteine S-methyltransferase involved in the conversion of S-adenosylmethionine (AdoMet) to methionine to control the methionine/AdoMet ratio. Converts also S- methylmethionine (SMM) to methionine
Gene Name:
MHT1
Uniprot ID:
Q12525
Molecular weight:
36714.5
Reactions
S-methyl-L-methionine + L-homocysteine → 2 L-methionine.
Protein Details
8. Homocysteine S-methyltransferase 2
General function:
Involved in homocysteine S-methyltransferase activity
Specific function:
Homocysteine S-methyltransferase involved in the conversion of S-adenosylmethionine (AdoMet) to methionine to control the methionine/AdoMet ratio. Converts also S- methylmethionine (SMM) to methionine
Gene Name:
SAM4
Uniprot ID:
Q08985
Molecular weight:
36668.19922
Reactions
S-methyl-L-methionine + L-homocysteine → 2 L-methionine.