(2S,3S)-2-Methylcitric acid (YMDB00978)

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Identification

YMDB ID

YMDB00978

Name

(2S,3S)-2-Methylcitric acid

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

(2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate is an extremely weak basic (essentially neutral) compound (based on its pKa) (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate exists in both E. coli (prokaryote) and yeast (eukaryote).

Structure

MOL SDF PDB SMILES InChI

Synonyms

(2S,3S)-2-methylcitrate
2-hydroxy-1,2,3-butanetricarboxylic acid
2-hydroxybutane-1,2,3-tricarboxylate
2-hydroxybutane-1,2,3-tricarboxylic acid
2-methylcitrate
2-methylcitric acid
(2S,3S)-2-Hydroxybutane-1,2,3-tricarboxylic acid
Methylcitric acid
3-Carboxy-3-hydroxy-2-methylpentanedioic acid
2-Methylcitric acid, 3H-labeled

CAS number

6061-96-7

Weight

Average: 206.1501
Monoisotopic: 206.042652674

InChI Key

YNOXCRMFGMSKIJ-NFNCENRGSA-N

InChI

InChI=1S/C7H10O7/c1-3(5(10)11)7(14,6(12)13)2-4(8)9/h3,14H,2H2,1H3,(H,8,9)(H,10,11)(H,12,13)/t3-,7+/m1/s1

IUPAC Name

(1S,2S)-2-hydroxy-1-methylpropane-1,2,3-tricarboxylic acid

Traditional IUPAC Name

(2S,3S)-2-methylcitric acid

Chemical Formula

C₇H₁₀O₇

SMILES

C[C@H](C(O)=O)[C@@](O)(CC(O)=O)C(O)=O

Chemical Taxonomy

Description

belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Tricarboxylic acids and derivatives

Direct Parent

Tricarboxylic acids and derivatives

Alternative Parents

Substituents

Tricarboxylic acid or derivatives
Hydroxy acid
Alpha-hydroxy acid
Tertiary alcohol
Carboxylic acid
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

2-methylcitric acid (CHEBI:50948 )

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	175 g/L	ALOGPS
logP	-0.89	ALOGPS
logP	-0.78	ChemAxon
logS	-0.07	ALOGPS
pKa (Strongest Acidic)	3.18	ChemAxon
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	132.13 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	40.2 m³·mol⁻¹	ChemAxon
Polarizability	17.33 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

mitochondrion

Organoleptic Properties

Not Available

SMPDB Pathways

Not Available

KEGG Pathways

Not Available

SMPDB Reactions

Not Available

KEGG Reactions

propionyl-CoA + water + Oxalacetic acid → (2S,3S)-2-Methylcitric acid + hydron + Coenzyme A

(2S,3S)-2-Methylcitric acid ↔ Methylisocitric acid

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0fer-4900000000-66b99961c9a1426fcc9e	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0900000000-be0da5c29220e9e50325	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-05i0-9600000000-2bead66ba2514df6497f	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-1093-7900000000-e7a5530b8562d859e032	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0900-1910000000-0a84eb8e0df2e6eb450d	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-07vi-4900000000-e89ea7de4d7e433cae1e	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9300000000-c68ffdf8bf6f5380005e	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
Pronk, J. T., van der Linden-Beuman, A., Verduyn, C., Scheffers, W. A., van Dijken, J. P. (1994). "Propionate metabolism in Saccharomyces cerevisiae: implications for the metabolon hypothesis." Microbiology 140 ( Pt 4):717-722.7912143
Gerike, U., Hough, D. W., Russell, N. J., Dyall-Smith, M. L., Danson, M. J. (1998). "Citrate synthase and 2-methylcitrate synthase: structural, functional and evolutionary relationships." Microbiology 144 ( Pt 4):929-935.9579066
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

Synthesis Reference:

Ewering, Christian; Braemer, Christian Oliver; Steinbuechel, Alexander. Production of 2-methylcitric acid by a recombinant Ralstonia eutropha strain. PCT Int. Appl. (2007), 30pp. CODEN: PIXXD2 WO 2007101866 A2 20070913 CAN 147:363646 AN 20

External Links:

Resource	Link
CHEBI ID	50948
HMDB ID	HMDB00379
Pubchem Compound ID	515
Kegg ID	Not Available
ChemSpider ID	24534242
FOODB ID	Not Available
Wikipedia ID	Not Available
BioCyc ID	Not Available

Enzymes

Protein Details

1. Citrate synthase 3

General function:: Involved in transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer
Specific function:: Acetyl-CoA + H(2)O + oxaloacetate = citrate + CoA
Gene Name:: CIT3
Uniprot ID:: P43635
Molecular weight:: 53810.69922

Reactions

Acetyl-CoA + H(2)O + oxaloacetate → citrate + CoA.
propanoyl-CoA + H2O + oxaloacetate → (2R,3S)-2-hydroxybutane-1,2,3-tricarboxylate + CoA

Protein Details

2. Probable 2-methylcitrate dehydratase

General function:: Involved in 2-methylcitrate dehydratase activity
Specific function:: Catalyzes the dehydration of 2-methylcitrate to 2- methyl-cis-aconitate
Gene Name:: PDH1
Uniprot ID:: Q12428
Molecular weight:: 57683.10156

Reactions

(2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate → (Z)-but-2-ene-1,2,3-tricarboxylate + H(2)O.

Structure for #<Compound:0xb67f2d88>

Enzymes

Reactions

Reactions