Succinic acid (YMDB00338)

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Identification

YMDB ID

YMDB00338

Name

Succinic acid

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Succinic acid, also known as butanedionic acid or succinate, belongs to the class of organic compounds known as dicarboxylic acids and derivatives. These are organic compounds containing exactly two carboxylic acid groups. Succinic acid exists in all living species, ranging from bacteria to plants to humans. Based on a literature review a significant number of articles have been published on Succinic acid.

Structure

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

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
Ammonium succinate
Butanedioic acid
Potassium succinate
Succinate, ammonium
Succinate, potassium
2-Acetamido-2-deoxy-D-glucose
D-GlcNAc
N-Acetyl-D-glucosamine
N-Acetylchitosamine
N Acetyl D glucosamine
2 Acetamido 2 deoxy D glucose
2 Acetamido 2 deoxyglucose
2-Acetamido-2-deoxyglucose
Acetylglucosamine

CAS number

110-15-6

Weight

Average: 118.088
Monoisotopic: 118.02660868

InChI Key

KDYFGRWQOYBRFD-UHFFFAOYSA-N

InChI

InChI=1S/C4H6O4/c5-3(6)1-2-4(7)8/h1-2H2,(H,5,6)(H,7,8)

IUPAC Name

butanedioic acid

Traditional IUPAC Name

succinic acid

Chemical Formula

C₄H₆O₄

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.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Dicarboxylic acids and derivatives

Direct Parent

Dicarboxylic 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 Framework

Aliphatic acyclic compounds

External Descriptors

C4-dicarboxylic acid (CHEBI:15741 )
alpha,omega-dicarboxylic acid (CHEBI:15741 )
Dicarboxylic acids (LMFA01170043 )

Physical Properties

State

Solid

Charge

Melting point

185-188 °C

Experimental Properties

Property	Value	Reference
Water Solubility	83.2 mg/mL at 25 oC [YALKOWSKY,SH & HE,Y (2003)]	PhysProp
LogP	-0.59 [HANSCH,C ET AL. (1995)]	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	211 g/L	ALOGPS
logP	-0.53	ALOGPS
logP	-0.4	ChemAxon
logS	0.25	ALOGPS
pKa (Strongest Acidic)	3.55	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	74.6 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	23.54 m³·mol⁻¹	ChemAxon
Polarizability	10.14 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

extracellular
mitochondrion
cytoplasm

Organoleptic Properties

Flavour/Odour	Source
Odorless	FDB001931
Sour	FDB001931

SMPDB Pathways

4-aminobutanoate degradation	PW002382
Citric Acid Cycle	PW000952
Citric Acid Cycle 1434561204	PW000970
Glutamate Metabolism	PW002376
Glyoxylate cycle	PW002419

KEGG Pathways

Alanine, aspartate and glutamate metabolism	ec00250
Butanoate metabolism	ec00650
Citrate cycle (TCA cycle)	ec00020
Glyoxylate and dicarboxylate metabolism	ec00630
Oxidative phosphorylation	ec00190

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 Concentration	Substrate	Growth Conditions	Strain	Citation
600 ± 30 µM	YEB media with 0.5 mM glucose	aerobic	Baker's yeast	Experimentally Determined Not Available
Conversion Details Here

Extracellular Concentrations

Intracellular Concentration	Substrate	Growth Conditions	Strain	Citation
577 ± 69 µM	hops, malted barley	anaerobic	Baker's yeast	PMID: 16448171
Conversion Details Here

Spectra

Spectrum Type	Description	Splash Key	View
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (2 TMS)	splash10-0002-0920000000-f286e6204a4163b823ba	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-0002-0900000000-bf336910bb37d7f78140	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (2 TMS)	splash10-006t-9800000000-df5ff4e8457d2d4ef919	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (2 TMS)	splash10-00c1-3930000000-3cc18e719822b5af661a	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-004i-9000000000-93b4807ae6275a3e59d7	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-0kos-9100000000-f1df0903a24c305e68ec	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-0002-0910000000-300c33b39fb991b5a73e	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0002-0920000000-f286e6204a4163b823ba	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0002-0900000000-bf336910bb37d7f78140	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-006t-9800000000-df5ff4e8457d2d4ef919	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-00c1-3930000000-3cc18e719822b5af661a	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0002-0900000000-f838d863ee7c2b111f02	JSpectraViewer \| MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-00xr-9300000000-f0644daf4fbb11fcc2dc	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-00dj-9710000000-ff8325384b9eefd19106	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Negative (Annotated)	splash10-00di-9300000000-f9dc864d93a09d3074f9	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Negative (Annotated)	splash10-00di-9300000000-76c151de384928b2256f	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Negative (Annotated)	splash10-01b9-7900000000-51d2341c097f04827944	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - EI-B (Unknown) , Positive	splash10-004i-9000000000-93b4807ae6275a3e59d7	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-03dj-0971010000-37d214dc7a8fdc26116b	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-014i-9000000000-249222ac742c1634cec9	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-00di-9000000000-6897d49472dba6a34a27	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-0udi-0490000000-d138f8023125921b4b82	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-014i-1900000000-4ffdabe5bde527b66982	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-00di-9100000000-c20baa818f5ff5f678c1	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-00di-9000000000-7a49a18aa6fcb2540a12	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-00di-9000000000-9955aeb0e5a9f88ae70e	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-00di-9000000000-7e1f195f111b4eafb4fa	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-00xr-9400000000-e50afc90e20cd420ba9b	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-00xr-9600000000-43167f2549cbb5d5f7e8	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-014i-1900000000-4ffdabe5bde527b66982	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-00di-9100000000-7a8bfa543dc087bea06d	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-00di-9000000000-fdec6c7458176f3cbeb8	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-00di-9000000000-9955aeb0e5a9f88ae70e	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0gb9-2900000000-9d959a53833b07094158	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0l6r-9600000000-c367e11e737714d41418	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-056r-9000000000-e65aa602a8293debec36	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-2900000000-e1f840494c9003279869	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-014i-7900000000-1089efd4a3469bcf14f1	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0604-9000000000-0e0e60bb202ffb004894	JSpectraViewer
MS	Mass Spectrum (Electron Ionization)	splash10-05di-9100000000-c629bea41d0d3d896425	JSpectraViewer \| MoNA
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H 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
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
2D NMR	[1H,1H] 2D NMR Spectrum	Not Available	JSpectraViewer
2D NMR	[1H,13C] 2D 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
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:

Resource	Link
CHEBI ID	15741
HMDB ID	HMDB00254
Pubchem Compound ID	1110
Kegg ID	C00042
ChemSpider ID	1078
FOODB ID	FDB001931
Wikipedia	Succinic_acid
BioCyc ID	SUC

(S)-dihydroorotate + O(2) → orotate + H(2)O(2).
(S)-dihydroorotate + a quinone → orotate + a quinol

Structure for #<Compound:0xae8b75a0>

Enzymes

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