Succinyl-CoA (YMDB00514)

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Identification

YMDB ID

YMDB00514

Name

Succinyl-CoA

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Succinyl-Coenzyme A belongs to the class of organic compounds known as acyl coas. These are organic compounds containing a coenzyme A substructure linked to an acyl chain. Thus, succinyl-coenzyme A is considered to be a fatty ester lipid molecule. Succinyl-Coenzyme A is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.

Structure

MOL SDF PDB SMILES InChI

Synonyms

CoA S-(hydrogen succinate)
CoA S-succinate
Coenzyme A S-(hydrogen succinate)
Coenzyme A S-succinate
S-(hydrogen butanedioate
S-(hydrogen butanedioate) CoA
S-(hydrogen butanedioate) Coenzyme A
S-(hydrogen butanedioic acid
S-Succinoylcoenzyme A
suc-co-A
suc-coa
succ-CoA
succ-Coenzyme A
succ-coenzyme-A
succ-S-CoA
succ-S-Coenzyme A
succ-S-coenzyme-A
succino-1-yl-coenzyme a
Succinyl CoA
Succinyl coenzyme A
succinyl-S-CoA
succinyl-S-Coenzyme A
succinyl-S-coenzyme-A
succinylcoenzyme-A
coenzyme A, S-(Hydrogen butanedioate)
S-(3-Carboxy-propionyl)-CoA
S-(3-Carboxy-propionyl)-coenzym-a
S-(3-Carboxypropionyl)-coenzyme A
S-(Hydrogen succinyl)-CoA
S-(Hydrogen succinyl)coenzyme A
coenzyme A, S-(Hydrogen butanedioic acid)
Succinyl-coenzyme A
Succinyl-CoA

CAS number

604-98-8

Weight

Average: 867.607
Monoisotopic: 867.131252359

InChI Key

VNOYUJKHFWYWIR-ITIYDSSPSA-N

InChI

InChI=1S/C25H40N7O19P3S/c1-25(2,20(38)23(39)28-6-5-14(33)27-7-8-55-16(36)4-3-15(34)35)10-48-54(45,46)51-53(43,44)47-9-13-19(50-52(40,41)42)18(37)24(49-13)32-12-31-17-21(26)29-11-30-22(17)32/h11-13,18-20,24,37-38H,3-10H2,1-2H3,(H,27,33)(H,28,39)(H,34,35)(H,43,44)(H,45,46)(H2,26,29,30)(H2,40,41,42)/t13-,18-,19-,20+,24-/m1/s1

IUPAC Name

4-[(2-{3-[(2R)-3-[({[({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)methyl]-2-hydroxy-3-methylbutanamido]propanamido}ethyl)sulfanyl]-4-oxobutanoic acid

Traditional IUPAC Name

succinyl-coa

Chemical Formula

C₂₅H₄₀N₇O₁₉P₃S

SMILES

CC(C)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)N1C=NC2=C1N=CN=C2N)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)CCC(O)=O

Chemical Taxonomy

Description

belongs to the class of organic compounds known as acyl coas. These are organic compounds containing a coenzyme A substructure linked to an acyl chain.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acyl thioesters

Direct Parent

Acyl CoAs

Alternative Parents

Substituents

Coenzyme a or derivatives
Purine ribonucleoside diphosphate
Purine ribonucleoside bisphosphate
Purine ribonucleoside 3',5'-bisphosphate
Ribonucleoside 3'-phosphate
Pentose-5-phosphate
Pentose phosphate
Glycosyl compound
N-glycosyl compound
Organic pyrophosphate
Pentose monosaccharide
6-aminopurine
Monosaccharide phosphate
Purine
Imidazopyrimidine
Hydroxy fatty acid
Thia fatty acid
Aminopyrimidine
Monoalkyl phosphate
Monosaccharide
N-substituted imidazole
Organic phosphoric acid derivative
Imidolactam
Phosphoric acid ester
Alkyl phosphate
Pyrimidine
Tetrahydrofuran
Azole
Imidazole
Heteroaromatic compound
Thiocarboxylic acid ester
Secondary alcohol
Carbothioic s-ester
Amino acid or derivatives
Amino acid
Thiocarboxylic acid or derivatives
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Sulfenyl compound
Carboximidic acid
Carboximidic acid derivative
Carboxylic acid derivative
Carboxylic acid
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Oxacycle
Azacycle
Organopnictogen compound
Organic oxide
Organic oxygen compound
Hydrocarbon derivative
Organosulfur compound
Organooxygen compound
Primary amine
Organic nitrogen compound
Alcohol
Amine
Carbonyl group
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

omega-carboxyacyl-CoA (CHEBI:15380 )

Physical Properties

State

Solid

Charge

Melting point

Not Available

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	3.84 g/L	ALOGPS
logP	-0.61	ALOGPS
logP	-6.1	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	0.82	ChemAxon
pKa (Strongest Basic)	4.24	ChemAxon
Physiological Charge	-5	ChemAxon
Hydrogen Acceptor Count	19	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	400.93 Å²	ChemAxon
Rotatable Bond Count	23	ChemAxon
Refractivity	183.1 m³·mol⁻¹	ChemAxon
Polarizability	77.46 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

mitochondrion
lipid particle
endoplasmic reticulum

Organoleptic Properties

Not Available

SMPDB Pathways

Citric Acid Cycle	PW000952
Citric Acid Cycle 1434561204	PW000970
Porphyrin Metabolism	PW002462
Sphingolipid metabolism	PW002479
TCA Cycle	PW002377

KEGG Pathways

Citrate cycle (TCA cycle)	ec00020
Glyoxylate and dicarboxylate metabolism	ec00630
Propanoate metabolism	ec00640
Sphingolipid metabolism	ec00600
Valine, leucine and isoleucine degradation	ec00280

SMPDB Reactions

Oxoglutaric acid + NAD + Coenzyme A → Succinyl-CoA + NADH + hydron + Carbon dioxide

Succinyl-CoA + phosphate + Guanosine diphosphate ↔ Succinic acid + Coenzyme A + GTP

Glycine + Succinyl-CoA → 5-Aminolevulinic acid + Carbon dioxide

Succinyl-CoA + Sphinganine → Dihydroceramide + Coenzyme A

Acetoacetic acid + Succinyl-CoA ↔ Succinic acid + acetoacetyl-CoA

KEGG Reactions

Glycine + hydron + Succinyl-CoA → 5-Aminolevulinic acid + Carbon dioxide + Coenzyme A

Coenzyme A + S(8)-succinyldihydrolipoamide → Dihydrolipoamide + Succinyl-CoA

Adenosine triphosphate + Coenzyme A + Succinic acid ↔ phosphate + ADP + Succinyl-CoA

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-1912000130-5d37f85b68294f1bcd7b	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-0913000000-5f3ce9a55c6b75d06990	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-2911000000-d4965f3bcf572b49e153	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-017j-8921150580-9a135870fabc65b05d2e	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-003s-4910010010-1b02ce20692d0ded522e	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-057i-6900100000-44f1bfaeb10b1463a0bd	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-0000000090-bb5a570be808ea8a3dd8	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00kg-9100001430-6a56696bfa6b84fc9826	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-016r-8102403910-3e8c6747e8bdbda6db09	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014r-0300000090-ce1ea17de736a3128d73	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-0901000020-307a08ff7ab07e0b6165	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-1119000000-859564ca28518883d359	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

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
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
Chelstowska, A., Rytka, J. (1993). "[Biosynthesis of heme in yeast Saccharomyces cerevisiae]." Postepy Biochem 39:173-185.8234090
Hoffman, M., Gora, M., Rytka, J. (2003). "Identification of rate-limiting steps in yeast heme biosynthesis." Biochem Biophys Res Commun 310:1247-1253.14559249
Ruttkay-Nedecky, B., Subik, J. (1990). "The OGD1 gene, affecting 2-oxoglutarate dehydrogenase in S. cerevisiae, is closely linked to HIS5 on chromosome IX." Curr Genet 17:85-88.2178788
Przybyla-Zawislak, B., Gadde, D. M., Ducharme, K., McCammon, M. T. (1999). "Genetic and biochemical interactions involving tricarboxylic acid cycle (TCA) function using a collection of mutants defective in all TCA cycle genes." Genetics 152:153-166.10224250
Przybyla-Zawislak, B., Dennis, R. A., Zakharkin, S. O., McCammon, M. T. (1998). "Genes of succinyl-CoA ligase from Saccharomyces cerevisiae." Eur J Biochem 258:736-743.9874242

Synthesis Reference:

Wollemann, M. Mechanism of the succinyl-coenzyme A synthesis in brain extracts. Acta Physiologica Academiae Scientiarum Hungaricae (1959), 16 153-4.

External Links:

Resource	Link
CHEBI ID	15380
HMDB ID	HMDB01022
Pubchem Compound ID	439161
Kegg ID	C00091
ChemSpider ID	24785295
FOODB ID	FDB022375
Wikipedia	Succinyl-CoA
BioCyc ID	3-METHYLBENZYLSUCCINYL-COA

Enzymes

Protein Details

1. 5-aminolevulinate synthase, mitochondrial

General function:: Involved in 5-aminolevulinate synthase activity
Specific function:: Succinyl-CoA + glycine = 5-aminolevulinate + CoA + CO(2)
Gene Name:: HEM1
Uniprot ID:: P09950
Molecular weight:: 59361.69922

Reactions

Succinyl-CoA + glycine → 5-aminolevulinate + CoA + CO(2).

Protein Details

2. Dihydrolipoyl dehydrogenase, mitochondrial

General function:: Involved in oxidoreductase activity
Specific function:: Lipoamide dehydrogenase is a component of the alpha- ketoacid dehydrogenase complexes. This includes the pyruvate dehydrogenase complex, which catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). Acts also as component of the glycine cleavage system (glycine decarboxylase complex), which catalyzes the degradation of glycine
Gene Name:: LPD1
Uniprot ID:: P09624
Molecular weight:: 54009.69922

Reactions

Protein N(6)-(dihydrolipoyl)lysine + NAD(+) → protein N(6)-(lipoyl)lysine + NADH.

Protein Details

3. Succinyl-CoA ligase [ADP-forming] subunit alpha, mitochondrial

General function:: Involved in catalytic activity
Specific function:: ATP + succinate + CoA = ADP + phosphate + succinyl-CoA
Gene Name:: LSC1
Uniprot ID:: P53598
Molecular weight:: 35032.19922

Reactions

ATP + succinate + CoA → ADP + phosphate + succinyl-CoA.

Protein Details

4. Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial

General function:: Involved in acyltransferase activity
Specific function:: The 2-oxoglutarate dehydrogenase complex catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). It contains multiple copies of three enzymatic components:2- oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3)
Gene Name:: KGD2
Uniprot ID:: P19262
Molecular weight:: 50430.30078

Reactions

Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine → CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine.

Protein Details

5. Sphingosine N-acyltransferase LAG1

General function:: Involved in protein binding
Specific function:: Component of the ceramide synthase complex required for C26-CoA-dependent ceramide synthesis. Redundant with LAC1. Facilitates ER-to-Golgi transport of GPI-anchored proteins. Involved in the aging process. Deletion of LAG1 results in a pronounced increase (approximately 50%) in mean and in maximum life span
Gene Name:: LAG1
Uniprot ID:: P38703
Molecular weight:: 48454.10156

Reactions

Acyl-CoA + sphingosine → CoA + N-acylsphingosine.

Protein Details

6. Sphingosine N-acyltransferase LAC1

General function:: Involved in identical protein binding
Specific function:: Component of the ceramide synthase complex required for C26-CoA-dependent ceramide synthesis. Redundant with LAG1. Facilitates ER-to-Golgi transport of GPI-anchored proteins
Gene Name:: LAC1
Uniprot ID:: P28496
Molecular weight:: 48991.60156

Reactions

Acyl-CoA + sphingosine → CoA + N-acylsphingosine.

Protein Details

7. Succinyl-CoA ligase [ADP-forming] subunit beta, mitochondrial

General function:: Involved in catalytic activity
Specific function:: ATP + succinate + CoA = ADP + phosphate + succinyl-CoA
Gene Name:: LSC2
Uniprot ID:: P53312
Molecular weight:: 46900.30078

Reactions

ATP + succinate + CoA → ADP + phosphate + succinyl-CoA.

Protein Details

8. Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial

General function:: Involved in acyltransferase activity
Specific function:: The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2)
Gene Name:: PDA2
Uniprot ID:: P12695
Molecular weight:: 51817.5

Reactions

Acetyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine → CoA + enzyme N(6)-(S-acetyldihydrolipoyl)lysine.

Protein Details

9. Glutathione reductase

General function:: Involved in oxidoreductase activity
Specific function:: Maintains high levels of reduced glutathione in the cytosol
Gene Name:: GLR1
Uniprot ID:: P41921
Molecular weight:: 53440.60156

Reactions

2 glutathione + NADP(+) → glutathione disulfide + NADPH.

Protein Details

10. 2-oxoglutarate dehydrogenase, mitochondrial

General function:: Involved in oxoglutarate dehydrogenase (succinyl-transferring) activity
Specific function:: The 2-oxoglutarate dehydrogenase complex catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). It contains multiple copies of three enzymatic components:2- oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3)
Gene Name:: KGD1
Uniprot ID:: P20967
Molecular weight:: 114416.0

Reactions

2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine → [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO(2).

Structure for #<Compound:0xaddce350>

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