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Succinic acid (YMDB00338)

Identification
YMDB IDYMDB00338
NameSuccinic acid
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionSuccinic acid is a dicarboxylic acid. The anion, succinate, is a component of the citric acid cycle.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 1,2-Ethanedicarboxylate
  • 1,2-Ethanedicarboxylic acid
  • 1,4-Butanedioate
  • 1,4-Butanedioic acid
  • Amber acid
  • Asuccin
  • butanedioic acid, ion(2-)
  • Dihydrofumarate
  • Dihydrofumaric acid
  • Katasuccin
  • Succinate
  • Wormwood acid
  • Acide butanedioique
  • Acide succinique
  • Acidum succinicum
  • Bernsteinsaeure
  • Butandisaeure
  • Butanedionic acid
  • e363
  • Ethylenesuccinic acid
  • HOOC-CH2-CH2-COOH
  • Spirit OF amber
  • Butanedionate
  • Ethylenesuccinate
  • 1,2 Ethanedicarboxylic acid
  • 1,4 Butanedioic acid
  • Potassium succinate
  • Succinate, ammonium
  • Butanedioic acid
  • Succinate, potassium
  • Ammonium succinate
CAS number110-15-6
WeightAverage: 118.088
Monoisotopic: 118.02660868
InChI KeyKDYFGRWQOYBRFD-UHFFFAOYSA-N
InChIInChI=1S/C4H6O4/c5-3(6)1-2-4(7)8/h1-2H2,(H,5,6)(H,7,8)
IUPAC Namebutanedioic acid
Traditional IUPAC Namesuccinic acid
Chemical FormulaC4H6O4
SMILES[H]OC(=O)C([H])([H])C([H])([H])C(=O)O[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as dicarboxylic acids and derivatives. These are organic compounds containing exactly two carboxylic acid groups.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassDicarboxylic acids and derivatives
Direct ParentDicarboxylic acids and derivatives
Alternative Parents
Substituents
  • Fatty acid
  • Dicarboxylic acid or derivatives
  • Carboxylic acid
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting point185-188 °C
Experimental Properties
PropertyValueReference
Water Solubility83.2 mg/mL at 25 oC [YALKOWSKY,SH & HE,Y (2003)]PhysProp
LogP-0.59 [HANSCH,C ET AL. (1995)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility211 g/LALOGPS
logP-0.53ALOGPS
logP-0.4ChemAxon
logS0.25ALOGPS
pKa (Strongest Acidic)3.55ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity23.54 m³·mol⁻¹ChemAxon
Polarizability10.14 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • extracellular
  • mitochondrion
  • cytoplasm
Organoleptic Properties
Flavour/OdourSource
OdorlessFDB001931
SourFDB001931
SMPDB Pathways
4-aminobutanoate degradationPW002382 ThumbThumb?image type=greyscaleThumb?image type=simple
Citric Acid CyclePW000952 ThumbThumb?image type=greyscaleThumb?image type=simple
Citric Acid Cycle 1434561204PW000970 ThumbThumb?image type=greyscaleThumb?image type=simple
Glutamate MetabolismPW002376 ThumbThumb?image type=greyscaleThumb?image type=simple
Glyoxylate cyclePW002419 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Alanine, aspartate and glutamate metabolismec00250 Map00250
Butanoate metabolismec00650 Map00650
Citrate cycle (TCA cycle)ec00020 Map00020
Glyoxylate and dicarboxylate metabolismec00630 Map00630
Oxidative phosphorylationec00190 Map00190
SMPDB Reactions
Succinyl-CoA + phosphate + Guanosine diphosphate ↔ Succinic acid + Coenzyme A + GTP
Succinic acid + Coenzyme Q10 + FAD ↔ Fumaric acid + QH2 + FADH2
Succinic acid semialdehyde + water + NADP → NADPH + Succinic acid + hydron
Succinic acid semialdehyde + NAD + water → Succinic acid + NADH + hydron
D-threo-Isocitric acid → Succinic acid + Glyoxylic acid
KEGG Reactions
Fumaric acid + L-Dihydroorotic acid → Orotic acid + Succinic acid
Fumaric acid + FADH2 → FAD + Succinic acid
Fumaric acid + FMNH2 ↔ Flavin Mononucleotide + Succinic acid
Isocitric acid → Glyoxylic acid + Succinic acid
Methylisocitric acid → Pyruvic acid + Succinic acid
Concentrations
Intracellular Concentrations
Intracellular ConcentrationSubstrateGrowth ConditionsStrainCitation
600 ± 30 µM YEB media with 0.5 mM glucoseaerobicBaker's yeastExperimentally Determined
Not Available
Conversion Details Here
Extracellular Concentrations
Intracellular ConcentrationSubstrateGrowth ConditionsStrainCitation
577 ± 69 µM hops, malted barleyanaerobicBaker's yeastPMID: 16448171
Conversion Details Here
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
  • Schwartz, J. M., Kanehisa, M. (2006). "Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis." BMC Bioinformatics 7:186.16584566
  • Luttik, M. A., Kotter, P., Salomons, F. A., van der Klei, I. J., van Dijken, J. P., Pronk, J. T. (2000). "The Saccharomyces cerevisiae ICL2 gene encodes a mitochondrial 2-methylisocitrate lyase involved in propionyl-coenzyme A metabolism." J Bacteriol 182:7007-7013.11092862
  • Takada, Y., Noguchi, T. (1985). "Characteristics of alanine: glyoxylate aminotransferase from Saccharomyces cerevisiae, a regulatory enzyme in the glyoxylate pathway of glycine and serine biosynthesis from tricarboxylic acid-cycle intermediates." Biochem J 231:157-163.3933486
  • 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
  • Almeida, C., Duarte, I. F., Barros, A., Rodrigues, J., Spraul, M., Gil, A. M. (2006). "Composition of beer by 1H NMR spectroscopy: effects of brewing site and date of production." J Agric Food Chem 54:700-706.16448171
  • Singh, J., Kumar, D., Ramakrishnan, N., Singhal, V., Jervis, J., Garst, J. F., Slaughter, S. M., DeSantis, A. M., Potts, M., Helm, R. F. (2005). "Transcriptional response of Saccharomyces cerevisiae to desiccation and rehydration." Appl Environ Microbiol 71:8752-8763.16332871
  • Palmieri, L., Lasorsa, F. M., De Palma, A., Palmieri, F., Runswick, M. J., Walker, J. E. (1997). "Identification of the yeast ACR1 gene product as a succinate-fumarate transporter essential for growth on ethanol or acetate." FEBS Lett 417:114-118.9395087
  • 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
  • Hogan, D. A., Auchtung, T. A., Hausinger, R. P. (1999). "Cloning and characterization of a sulfonate/alpha-ketoglutarate dioxygenase from Saccharomyces cerevisiae." J Bacteriol 181:5876-5879.10482536
  • Nagy, M., Lacroute, F., Thomas, D. (1992). "Divergent evolution of pyrimidine biosynthesis between anaerobic and aerobic yeasts." Proc Natl Acad Sci U S A 89:8966-8970.1409592
  • Coleman, S. T., Fang, T. K., Rovinsky, S. A., Turano, F. J., Moye-Rowley, W. S. (2001). "Expression of a glutamate decarboxylase homologue is required for normal oxidative stress tolerance in Saccharomyces cerevisiae." J Biol Chem 276:244-250.11031268
  • Muratsubaki, H., Enomoto, K. (1998). "One of the fumarate reductase isoenzymes from Saccharomyces cerevisiae is encoded by the OSM1 gene." Arch Biochem Biophys 352:175-181.9587404
  • 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:Berglund, Kris Arvid; Andersson, Christian; Rova, Ulrika. Process for the production of succinic acid. PCT Int. Appl. (2007), 30pp.
External Links:
ResourceLink
CHEBI ID15741
HMDB IDHMDB00254
Pubchem Compound ID1110
Kegg IDC00042
ChemSpider ID1078
FOODB IDFDB001931
WikipediaSuccinic_acid
BioCyc IDSUC

Enzymes

Protein Details
1. Isocitrate lyase
General function:
Involved in isocitrate lyase activity
Specific function:
Catalyzes the formation of succinate and glyoxylate from isocitrate, a key step of the glyoxylate cycle, which operates as an anaplerotic route for replenishing the tricarboxylic acid cycle. Required for growth on ethanol or acetate, but dispensable when fermentable carbon sources are available. Acts also on 2- methylisocitrate
Gene Name:
ICL1
Uniprot ID:
P28240
Molecular weight:
62408.30078
Reactions
Isocitrate → succinate + glyoxylate.
Protein Details
2. 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
3. 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
4. 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
5. 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
6. 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
7. Fumarate reductase
General function:
Involved in electron carrier activity
Specific function:
Could be a fumarate reductase
Gene Name:
Not Available
Uniprot ID:
P32614
Molecular weight:
50843.69922
Reactions
Succinate + NAD(+) → fumarate + NADH.
Protein Details
8. Osmotic growth protein 1
General function:
Involved in electron carrier activity
Specific function:
Could be a fumarate reductase
Gene Name:
OSM1
Uniprot ID:
P21375
Molecular weight:
55064.80078
Reactions
Protein Details
9. Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
General function:
Involved in electron carrier activity
Specific function:
Catalytic subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q). SDH1 and SDH2 form the catalytic dimer. Electrons flow from succinate to the FAD bound to SDH1, and sequentially through the iron-sulfur clusters bound to SDH2 and enter the membrane dimer formed by SDH3 and SDH4
Gene Name:
SDH1
Uniprot ID:
Q00711
Molecular weight:
70228.79688
Reactions
Succinate + ubiquinone → fumarate + ubiquinol.
Protein Details
10. Succinate dehydrogenase [ubiquinone] flavoprotein subunit 2, mitochondrial
General function:
Involved in electron carrier activity
Specific function:
Probable minor catalytic subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q). Probably forms a catalytic dimer with SDH2. Electrons flow from succinate to the FAD bound to the catalytic subunit, and sequentially through the iron-sulfur clusters bound to SDH2 and enter the membrane dimer formed by SDH3 and SDH4
Gene Name:
Not Available
Uniprot ID:
P47052
Molecular weight:
69382.0
Reactions
Succinate + ubiquinone → fumarate + ubiquinol.
Protein Details
11. Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
General function:
Involved in 2 iron, 2 sulfur cluster binding
Specific function:
Subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q). SDH1 and SDH2 form the catalytic dimer. Electrons flow from succinate to the FAD bound to SDH1, and sequentially through the iron-sulfur clusters bound to SDH2 and enter the membrane dimer formed by SDH3 and SDH4
Gene Name:
SDH2
Uniprot ID:
P21801
Molecular weight:
30230.90039
Reactions
Succinate + ubiquinone → fumarate + ubiquinol.
Protein Details
12. Mitochondrial 2-methylisocitrate lyase
General function:
Involved in isocitrate lyase activity
Specific function:
Catalyzes the formation of pyruvate and succinate from 2-methylisocitrate during the metabolism of endogenous propionyl- CoA. Does not act on isocitrate
Gene Name:
ICL2
Uniprot ID:
Q12031
Molecular weight:
64975.39844
Reactions
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate → pyruvate + succinate.
Protein Details
13. Alpha-ketoglutarate-dependent sulfonate dioxygenase
General function:
Involved in oxidoreductase activity
Specific function:
Acts as a alpha-ketoglutarate-dependent dioxygenase active on sulfonates. Although taurine is a poor substrate, a variety of other sulfonates are utilized, with the best natural substrates being isethionate and taurocholate
Gene Name:
JLP1
Uniprot ID:
Q12358
Molecular weight:
46982.30078
Reactions
Protein Details
14. Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
(S)-1-pyrroline-5-carboxylate + NAD(P)(+) + 2 H(2)O = L-glutamate + NAD(P)H
Gene Name:
PUT2
Uniprot ID:
P07275
Molecular weight:
64434.60156
Reactions
(S)-1-pyrroline-5-carboxylate + NAD(P)(+) + 2 H(2)O → L-glutamate + NAD(P)H.
Protein Details
15. Succinate-semialdehyde dehydrogenase [NADP+]
General function:
Involved in oxidoreductase activity
Specific function:
Succinate semialdehyde + NAD(P)(+) + H(2)O = succinate + NAD(P)H
Gene Name:
UGA2
Uniprot ID:
P38067
Molecular weight:
54188.80078
Reactions
Succinate semialdehyde + NAD(P)(+) + H(2)O → succinate + NAD(P)H.
Protein Details
16. Dihydroorotate dehydrogenase
General function:
Involved in catalytic activity
Specific function:
In the de novo pyrimidine biosynthesic pathway, catalyzes the stereospecific oxidation of (S)-dihydroorotate to orotate and the reduction of fumarate to succinate. Does not use oxaloacetate and NAD or NADP as electron acceptors
Gene Name:
URA1
Uniprot ID:
P28272
Molecular weight:
34800.60156
Reactions
(S)-dihydroorotate + O(2) → orotate + H(2)O(2).
(S)-dihydroorotate + a quinone → orotate + a quinol

Transporters

Protein Details
1. Succinate/fumarate mitochondrial transporter
General function:
Involved in binding
Specific function:
Transports cytoplasmic succinate, derived from isocitrate by the action of isocitrate lyase in the cytosol, into the mitochondrial matrix in exchange for fumarate
Gene Name:
SFC1
Uniprot ID:
P33303
Molecular weight:
35340.10156
Protein Details
2. Mitochondrial dicarboxylate transporter
General function:
Involved in antiporter activity
Specific function:
Mitochondrial dicarboxylic transporter catalyzing the exchange of dicarboxylic acids like malate and succinate for inorganic phosphate. Required for growth on ethanol and acetate
Gene Name:
DIC1
Uniprot ID:
Q06143
Molecular weight:
32991.30078