ECMDB: L-Homocysteine (ECMDB00165) (M2MDB000067)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (7)XML

Proteins (2463)

Record Information

Version

2.0

Creation Date

2012-05-31 10:22:38 -0600

Update Date

2015-09-13 12:56:06 -0600

Secondary Accession Numbers

ECMDB00165

Identification

Name:

L-Homocysteine

Description

Homocysteine is a thiol-containing amino acid formed by a demethylation of methionine. Homocysteine is a variant of the amino acid cysteine, differing in that its side-chain contains an additional methylene (-CH2-) group before the thiol (-SH) group. In Escherichia coli homocysteine (Hcy) is the last intermediate on the methionine biosynthetic pathway.

Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms:

(+-)-homocysteine
(S)-2-amino-4-mercapto-Butanoate
(S)-2-amino-4-mercapto-Butanoic acid
(S)-2-Amino-4-mercaptobutanoate
(S)-2-Amino-4-mercaptobutanoic acid
(S)-Homocysteine
2-amino-4-mercapto-Butanoate
2-amino-4-mercapto-Butanoic acid
2-Amino-4-mercapto-Butyrate
2-Amino-4-mercapto-Butyric acid
2-amino-4-mercapto-DL-Butyrate
2-amino-4-mercapto-DL-Butyric acid
2-Amino-4-mercapto-L-butyrate
2-Amino-4-mercapto-L-butyric acid
2-Amino-4-mercaptobutyrate
2-Amino-4-mercaptobutyric acid
2-amino-4-sulfanylbutanoate
2-amino-4-sulfanylbutanoic acid
2-amino-4-Sulphanylbutanoate
2-amino-4-Sulphanylbutanoic acid
D,l-homocysteine
DL-2-amino-4-mercapto-Butyrate
DL-2-amino-4-mercapto-Butyric acid
DL-2-amino-4-Mercaptobutyrate
DL-2-Amino-4-mercaptobutyric acid
DL-Homocysteine
DL-homocysteine (free base)
HCY
Homo-cys
Homocysteine
L-2-Amino-4-mercapto-Butyrate
L-2-Amino-4-mercapto-Butyric acid
L-2-Amino-4-mercaptobutyrate
L-2-Amino-4-mercaptobutyric acid
L-Homocysteine
Usaf B-12

Chemical Formula:

C₄H₉NO₂S

Weight:

Average: 135.185
Monoisotopic: 135.035399227

InChI Key:

FFFHZYDWPBMWHY-VKHMYHEASA-N

InChI:

InChI=1S/C4H9NO2S/c5-3(1-2-8)4(6)7/h3,8H,1-2,5H2,(H,6,7)/t3-/m0/s1

CAS number:

6027-13-0

IUPAC Name:

(2S)-2-amino-4-sulfanylbutanoic acid

Traditional IUPAC Name:

L-homocysteine

SMILES:

N[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.

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
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 Framework

Aliphatic acyclic compounds

External Descriptors

homocysteine (CHEBI:17588 )
serine family amino acid (CHEBI:17588 )
Other amino acids (C00155 )

Physical Properties

State:

Solid

Charge:

Melting point:

232.6 °C

Experimental Properties:

Property	Value	Source
LogP:	-2.538	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	14.8 g/L	ALOGPS
logP	-2.3	ALOGPS
logP	-2.6	ChemAxon
logS	-0.96	ALOGPS
pKa (Strongest Acidic)	2.46	ChemAxon
pKa (Strongest Basic)	9.41	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	63.32 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	32.93 m³·mol⁻¹	ChemAxon
Polarizability	13.54 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

Reactions:

L-Cystathionine + Water > L-Homocysteine + Ammonium + Pyruvic acid
5-Methyltetrahydrofolic acid + L-Homocysteine <> Hydrogen ion + L-Methionine + Tetrahydrofolic acid
L-Homocysteine + S-Methylmethionine > Hydrogen ion +2 L-Methionine
S-Adenosylmethionine + L-Homocysteine + S-Methylmethionine <> S-Adenosylhomocysteine + Hydrogen ion + L-Methionine
S-Ribosyl-L-homocysteine > 4,5-Dihydroxy-2,3-pentanedione + L-Homocysteine
S-Adenosylmethionine + L-Homocysteine <> S-Adenosylhomocysteine + L-Methionine
5-Methyltetrahydrofolic acid + L-Homocysteine <> Tetrahydrofolic acid + L-Methionine
Cystathionine + Water <> L-Homocysteine + Ammonia + Pyruvic acid
L-Cystathionine + Water <> L-Homocysteine + Ammonia + Pyruvic acid
O-Succinyl-L-homoserine + Hydrogen sulfide <> L-Homocysteine + Succinic acid
S-Ribosyl-L-homocysteine <> (4S)-4,5-Dihydroxypentan-2,3-dione + L-Homocysteine
5-Methyltetrahydropteroyltri-L-glutamic acid + L-Homocysteine <> Tetrahydropteroyltri-L-glutamic acid + L-Methionine
L-Cystathionine + Water > Hydrogen ion + Pyruvic acid + Ammonia + L-Homocysteine
L-Homocysteine + 5-Methyltetrahydropteroyltri-L-glutamic acid > L-Methionine + tetrahydropteroyl tri-L-glutamate
L-Homocysteine + 5-Methyltetrahydrofolic acid L-Methionine + Tetrahydrofolic acid
L-Homocysteine + S-Adenosylmethionine Hydrogen ion + L-Methionine + S-Adenosylhomocysteine
S-methyl-L-methionine + L-Homocysteine Hydrogen ion + L-Methionine
S-Ribosyl-L-homocysteine > L-Homocysteine + (4S)-4,5-Dihydroxypentan-2,3-dione
L-Cystathionine + Water > L-Homocysteine + Ammonia + Pyruvic acid
5-methyltetrahydropteroyltri-L-glutamate + L-Homocysteine > tetrahydropteroyltri-L-glutamate + L-Methionine
5-Methyltetrahydrofolic acid + L-Homocysteine > Tetrahydrofolic acid + L-Methionine
S-methyl-L-methionine + L-Homocysteine >2 L-Methionine
L-Cystathionine + Water + 2-Aminoacrylic acid + 2-Iminopropanoate <> L-Homocysteine + Pyruvic acid + Ammonia
5 5-Methyltetrahydrofolic acid + L-Homocysteine <> Hydrogen ion + L-Methionine + Tetrahydrofolic acid
5 5-Methyltetrahydrofolic acid + L-Homocysteine <> Hydrogen ion + L-Methionine + Tetrahydrofolic acid

SMPDB Pathways:

Nitrogen metabolism	PW000755
One carbon pool by folate	PW000773
Sulfur metabolism	PW000922

KEGG Pathways:

Cysteine and methionine metabolism ec00270
Metabolic pathways eco01100
Nitrogen metabolism ec00910
One carbon pool by folate ec00670
Selenoamino acid metabolism ec00450
Sulfur metabolism ec00920

EcoCyc Pathways:

S-adenosyl-L-methionine cycle I PWY-6151
autoinducer AI-2 biosynthesis I PWY-6153
formylTHF biosynthesis I 1CMET2-PWY
methionine biosynthesis I HOMOSER-METSYN-PWY

Concentrations

Concentration	Strain	Media	Growth Status	Growth System	Temperature	Details
370± 0 uM	K12 NCM3722	Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glucose	Mid-Log Phase	Shake flask and filter culture	37 oC	PMID: 19561621

Find out more about how we convert literature concentrations.

Spectra

Spectra:

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-004i-0920000000-20fbffbe76510c066e6f	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9000000000-1f800d28bca4b2b7a49f	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , positive	splash10-014l-4900000000-c50d79ba3a5013bcf29f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , positive	splash10-000i-9000000000-025c9e1f4fb58138c43b	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , positive	splash10-014i-4900000000-33f205e002f49f034764	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-052r-0900000000-c1f98c8182b5ddc09cb1	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00ko-9800000000-80a1c80328e8836233a4	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0006-9100000000-1f611da44349ffdfaefe	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0bvi-9000000000-c9d62a66522e46a17f56	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-3900000000-e8322d5858cba16a3bd2	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00lr-6900000000-e0190a1cc33e605bac0a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-001i-9000000000-900bb5d8fb11bec02e39	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-0900000000-38e427e24202b2411597	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001i-7900000000-5cf2133d9faac56032d3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-001i-9000000000-942ac689538269d6ca7b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0006-9000000000-166428542631f9ac0714	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a4i-9000000000-9bcb57b924579a6c3411	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4j-9000000000-8eee886864db64f3eec2	View in MoNA
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	View in JSpectraViewer

References

References:

Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. Pubmed: 19561621
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
Vijayendran, C., Barsch, A., Friehs, K., Niehaus, K., Becker, A., Flaschel, E. (2008). "Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling." Genome Biol 9:R72. Pubmed: 18402659
Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064

Synthesis Reference:

Biochem Prepn. 5 93 (1957)

Material Safety Data Sheet (MSDS)

Download (PDF)

Links

External Links:

Resource	Link
CHEBI ID	17588
HMDB ID	HMDB00742
Pubchem Compound ID	91552
Kegg ID	C00155
ChemSpider ID	82666
Wikipedia	Homocysteine
BioCyc ID	HOMO-CYS
EcoCyc ID	HOMO-CYS
Ligand Expo	HCS

Enzymes

Protein Details

1. Cystathionine gamma-synthase

General function:: Involved in pyridoxal phosphate binding
Specific function:: O(4)-succinyl-L-homoserine + L-cysteine = L- cystathionine + succinate
Gene Name:: metB
Uniprot ID:: P00935
Molecular weight:: 41550

Reactions

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

Protein Details

2. Cystathionine beta-lyase metC

General function:: Involved in pyridoxal phosphate binding
Specific function:: L-cystathionine + H(2)O = L-homocysteine + NH(3) + pyruvate
Gene Name:: metC
Uniprot ID:: P06721
Molecular weight:: 43212

Reactions

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

Protein Details

3. Methionine synthase

General function:: Involved in methionine synthase activity
Specific function:: Catalyzes the transfer of a methyl group from methyl- cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Subsequently, remethylates the cofactor using methyltetrahydrofolate
Gene Name:: metH
Uniprot ID:: P13009
Molecular weight:: 135996

Reactions

5-methyltetrahydrofolate + L-homocysteine = tetrahydrofolate + L-methionine.

Protein Details

4. Protein malY

General function:: Involved in transferase activity
Specific function:: Acts as a beta-cystathionase and as a repressor of the maltose regulon
Gene Name:: malY
Uniprot ID:: P23256
Molecular weight:: 43641

Reactions

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

Protein Details

5. 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:: metE
Uniprot ID:: P25665
Molecular weight:: 84673

Reactions

5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = tetrahydropteroyltri-L-glutamate + L-methionine.

Protein Details

6. S-ribosylhomocysteine lyase

General function:: Involved in catalytic activity
Specific function:: Involved in the synthesis of autoinducer 2 (AI-2) which is secreted by bacteria and is used to communicate both the cell density and the metabolic potential of the environment. The regulation of gene expression in response to changes in cell density is called quorum sensing. Catalyzes the transformation of S-ribosylhomocysteine (RHC) to homocysteine (HC) and 4,5- dihydroxy-2,3-pentadione (DPD)
Gene Name:: luxS
Uniprot ID:: P45578
Molecular weight:: 19416

Reactions

S-(5-deoxy-D-ribos-5-yl)-L-homocysteine = L-homocysteine + (4S)-4,5-dihydroxypentan-2,3-dione.

Protein Details

7. Homocysteine S-methyltransferase

General function:: Involved in homocysteine S-methyltransferase activity
Specific function:: Catalyzes methyl transfer from S-methylmethionine or S- adenosylmethionine (less efficient) to homocysteine, selenohomocysteine and less efficiently selenocysteine
Gene Name:: mmuM
Uniprot ID:: Q47690
Molecular weight:: 33422

Reactions

S-methyl-L-methionine + L-homocysteine = 2 L-methionine.

L-Homocysteine (ECMDB00165) (M2MDB000067)

Structure for #<Compound:0x9db7d430>

Enzymes

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