Canmetcon
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Identification
YMDB IDYMDB00514
NameSuccinyl-CoA
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionSuccinyl-CoA is an important intermediate in the citric acid cycle, where it is synthesized from alpha-ketoglutarate by alpha-ketoglutarate dehydrogenase [EC 1.2.4.2] through decarboxylation. It is then converted into succinate through the hydrolytic release of coenzyme A by succinyl-CoA synthetase [EC 6.2.1.5].
Structure
Thumb
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
  • SUCCINYL-coenzyme A
  • coenzyme A, S-(Hydrogen butanedioic acid)
CAS number604-98-8
WeightAverage: 867.607
Monoisotopic: 867.131252359
InChI KeyVNOYUJKHFWYWIR-ITIYDSSPSA-N
InChIInChI=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 Name4-[(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 Namesuccinyl-coa
Chemical FormulaC25H40N7O19P3S
SMILESCC(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
DescriptionThis compound 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.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acyl thioesters
Direct ParentAcyl CoAs
Alternative Parents
Substituents
  • Coenzyme a or derivatives
  • Purine ribonucleoside diphosphate
  • Purine ribonucleoside 3',5'-bisphosphate
  • N-glycosyl compound
  • Glycosyl compound
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • 6-aminopurine
  • Purine
  • Imidazopyrimidine
  • Monoalkyl phosphate
  • Thia fatty acid
  • Aminopyrimidine
  • Imidolactam
  • Alkyl phosphate
  • Pyrimidine
  • Primary aromatic amine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • N-substituted imidazole
  • Monosaccharide
  • Saccharide
  • Heteroaromatic compound
  • Oxolane
  • Imidazole
  • Azole
  • Thiocarboxylic acid ester
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Sulfenyl compound
  • Thioether
  • Thiocarboxylic acid or derivatives
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Carboximidic acid derivative
  • Carboximidic acid
  • Hydrocarbon derivative
  • Primary amine
  • Organosulfur compound
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Amine
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility3.84 g/LALOGPS
logP-0.61ALOGPS
logP-7.2ChemAxon
logS-2.4ALOGPS
pKa (Strongest Acidic)0.82ChemAxon
pKa (Strongest Basic)4.98ChemAxon
Physiological Charge-5ChemAxon
Hydrogen Acceptor Count19ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area400.93 ŲChemAxon
Rotatable Bond Count23ChemAxon
Refractivity183.1 m³·mol⁻¹ChemAxon
Polarizability76.92 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • mitochondrion
  • lipid particle
  • endoplasmic reticulum
Organoleptic PropertiesNot Available
SMPDB Pathways
Citric Acid CyclePW000952 ThumbThumb?image type=greyscaleThumb?image type=simple
Citric Acid Cycle 1434561204PW000970 ThumbThumb?image type=greyscaleThumb?image type=simple
Porphyrin MetabolismPW002462 ThumbThumb?image type=greyscaleThumb?image type=simple
Sphingolipid metabolismPW002479 ThumbThumb?image type=greyscaleThumb?image type=simple
TCA CyclePW002377 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Citrate cycle (TCA cycle)ec00020 Map00020
Glyoxylate and dicarboxylate metabolismec00630 Map00630
Propanoate metabolismec00640 Map00640
Sphingolipid metabolismec00600 Map00600
Valine, leucine and isoleucine degradationec00280 Map00280
SMPDB Reactions
Oxoglutaric acid + NAD + Coenzyme ASuccinyl-CoA + NADH + hydron + Carbon dioxide
Succinyl-CoA + phosphate + Guanosine diphosphateSuccinic acid + Coenzyme A + GTP
Glycine + Succinyl-CoA5-Aminolevulinic acid + Carbon dioxide
Succinyl-CoA + SphinganineDihydroceramide + Coenzyme A
Acetoacetic acid + Succinyl-CoASuccinic acid + acetoacetyl-CoA
KEGG Reactions
Glycine + hydron + Succinyl-CoA5-Aminolevulinic acid + Carbon dioxide + Coenzyme A
Coenzyme A + S(8)-succinyldihydrolipoamideDihydrolipoamide + Succinyl-CoA
Adenosine triphosphate + Coenzyme A + Succinic acidphosphate + ADP + Succinyl-CoA
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
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:
ResourceLink
CHEBI ID15380
HMDB IDHMDB01022
Pubchem Compound ID439161
Kegg IDC00091
ChemSpider ID24785295
FOODB IDNot Available
WikipediaSuccinyl-CoA
BioCyc ID3-METHYLBENZYLSUCCINYL-COA

Enzymes

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).
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.
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.
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.
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.
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.
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.
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.
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.
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).