malonyl-CoA (YMDB00533)

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Identification

YMDB ID

YMDB00533

Name

malonyl-CoA

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

malonyl-CoA belongs to the class of organic compounds known as monoalkyl phosphates. These are organic compounds containing a phosphate group that is linked to exactly one alkyl chain. Thus, malonyl-CoA is considered to be a fatty ester lipid molecule. malonyl-CoA is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. malonyl-CoA exists in both E. coli (prokaryote) and yeast (eukaryote). Within yeast, malonyl-CoA participates in a number of enzymatic reactions. In particular, palmityl-CoA and malonyl-CoA can be converted into 3-oxooctadecanoyl-CoA through its interaction with the enzyme 3-ketoacyl-CoA synthase ELO1. In addition, eicosanoyl-CoA and malonyl-CoA can be converted into 3-oxodocosanoyl-CoA through the action of the enzyme 3-ketoacyl-CoA synthase ELO1. In yeast, malonyl-CoA is involved in the metabolic pathway called biosynthesis of unsaturated fatty acids pathway.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Malonyl CoA
Malonyl Coenzyme A
malonyl-CoA
malonyl-Coenzyme A
omega-Carboxyacyl-CoA
omega-Carboxyacyl-Coenzyme A
S-(Hydrogen malonyl)coenzyme A
S-(hydrogen propanedioate
S-(hydrogen propanedioate) CoA
S-(hydrogen propanedioate) Coenzyme A
S-(hydrogen propanedioic acid
coenzyme A, S-(Hydrogen propanedioate)
coenzyme A, S-(Hydrogen propanedioic acid)
CoA, Malonyl
coenzyme A, Malonyl

CAS number

524-14-1

Weight

Average: 853.58
Monoisotopic: 853.115602295

InChI Key

LTYOQGRJFJAKNA-DVVLENMVSA-N

InChI

InChI=1S/C24H38N7O19P3S/c1-24(2,19(37)22(38)27-4-3-13(32)26-5-6-54-15(35)7-14(33)34)9-47-53(44,45)50-52(42,43)46-8-12-18(49-51(39,40)41)17(36)23(48-12)31-11-30-16-20(25)28-10-29-21(16)31/h10-12,17-19,23,36-37H,3-9H2,1-2H3,(H,26,32)(H,27,38)(H,33,34)(H,42,43)(H,44,45)(H2,25,28,29)(H2,39,40,41)/t12-,17-,18-,19+,23-/m1/s1

IUPAC Name

3-[(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]-3-oxopropanoic acid

Traditional IUPAC Name

malonyl-coa

Chemical Formula

C₂₄H₃₈N₇O₁₉P₃S

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)CC(O)=O

Chemical Taxonomy

Description

belongs to the class of organic compounds known as monoalkyl phosphates. These are organic compounds containing a phosphate group that is linked to exactly one alkyl chain.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Organic phosphoric acids and derivatives

Sub Class

Phosphate esters

Direct Parent

Monoalkyl phosphates

Alternative Parents

Substituents

Monoalkyl phosphate
Short-chain hydroxy acid
Fatty acid
Tertiary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

primary alcohol (CHEBI:17436 )
carboxyalkyl phosphate (CHEBI:17436 )
Hydroxy fatty acids (LMFA01050415 )

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	3.8 g/L	ALOGPS
logP	-0.62	ALOGPS
logP	-7.1	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	0.82	ChemAxon
pKa (Strongest Basic)	4.97	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	22	ChemAxon
Refractivity	178.55 m³·mol⁻¹	ChemAxon
Polarizability	74.68 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
cytoplasm

Organoleptic Properties

Not Available

SMPDB Pathways

Biosynthesis of unsaturated fatty acids	PW002403
Biosynthesis of unsaturated fatty acids (docosanoyl)	PW002408
Biosynthesis of unsaturated fatty acids (icosanoyl)	PW002434
Biosynthesis of unsaturated fatty acids (stearoyl)	PW002435
Biosynthesis of unsaturated fatty acids (tetracosanoyl-CoA)	PW002404

KEGG Pathways

Biosynthesis of unsaturated fatty acids	ec01040
Fatty acid biosynthesis	ec00061
Phenylalanine metabolism	ec00360
Propanoate metabolism	ec00640
Pyruvate metabolism	ec00620

SMPDB Reactions

KEGG Reactions

Carbonic acid + Adenosine triphosphate + Acetyl-CoA ↔ phosphate + malonyl-CoA + hydron + ADP

malonyl-CoA + Caprylic acid + hydron + NADPH → capric acid + Carbon dioxide + NADP + water + Coenzyme A

capric acid + malonyl-CoA + hydron + NADPH → lauric acid + Carbon dioxide + NADP + water + Coenzyme A

lauric acid + malonyl-CoA + hydron + NADPH → Carbon dioxide + NADP + myristic acid + water + Coenzyme A

lauric acid + hydron + malonyl-CoA + oxygen + NADPH → NADP + Carbon dioxide + Myristoleic acid + Coenzyme A + water

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-da8095652669b99c8349	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-0913000000-c93bc8aa729d6712ed08	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-2911000000-dee360a0ee5e683d782c	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-9830140570-8e78a24b9858f67c1579	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001i-5910010010-97fdf25aafbfdff7c908	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-057i-6900100000-33483ed329c67d3c4cac	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
Dickson, R. C., Sumanasekera, C., Lester, R. L. (2006). "Functions and metabolism of sphingolipids in Saccharomyces cerevisiae." Prog Lipid Res 45:447-465.16730802
Hoja, U., Marthol, S., Hofmann, J., Stegner, S., Schulz, R., Meier, S., Greiner, E., Schweizer, E. (2004). "HFA1 encoding an organelle-specific acetyl-CoA carboxylase controls mitochondrial fatty acid synthesis in Saccharomyces cerevisiae." J Biol Chem 279:21779-21786.14761959
Kohlwein, S. D., Eder, S., Oh, C. S., Martin, C. E., Gable, K., Bacikova, D., Dunn, T. (2001). "Tsc13p is required for fatty acid elongation and localizes to a novel structure at the nuclear-vacuolar interface in Saccharomyces cerevisiae." Mol Cell Biol 21:109-125.11113186
Schneiter, R., Tatzer, V., Gogg, G., Leitner, E., Kohlwein, S. D. (2000). "Elo1p-dependent carboxy-terminal elongation of C14:1Delta(9) to C16:1Delta(11) fatty acids in Saccharomyces cerevisiae." J Bacteriol 182:3655-3660.10850979
Kastaniotis, A. J., Autio, K. J., Sormunen, R. T., Hiltunen, J. K. (2004). "Htd2p/Yhr067p is a yeast 3-hydroxyacyl-ACP dehydratase essential for mitochondrial function and morphology." Mol Microbiol 53:1407-1421.15387819

Synthesis Reference:

Hulsmann, W. C. Synthesis of malonyl coenzyme A from acetyl coenzyme A and oxalosuccinate in mitochondria. Biochimica et Biophysica Acta (1963), 77(3), 502-3.

External Links:

Resource	Link
CHEBI ID	15531
HMDB ID	HMDB01175
Pubchem Compound ID	10663
Kegg ID	C00083
ChemSpider ID	24785730
FOODB ID	FDB030990
Wikipedia	Malonyl-CoA
BioCyc ID	MALONYL-COA

Enzymes

Protein Details

1. Elongation of fatty acids protein 2

General function:: Involved in fatty acid elongase activity
Specific function:: Involved in synthesis of 1,3-beta-glucan. Could be a subunit of 1,3-beta-glucan synthase. Could be also a component of the membrane bound fatty acid elongation systems that produce the 26-carbon very long chain fatty acids that are precursors for ceramide and sphingolipids. Appears to be involved in the elongation of fatty acids up to 24 carbons. Appears to have the highest affinity for substrates with chain length less than 22 carbons
Gene Name:: FEN1
Uniprot ID:: P25358
Molecular weight:: 40001.80078

Reactions

Acyl-CoA + malonyl-CoA → 3-oxoacyl-CoA + CoA + CO(2).

Protein Details

2. Elongation of fatty acids protein 1

General function:: Involved in fatty acid elongase activity
Specific function:: May be a membrane bound enzyme involved in the highly specific elongation of saturated 14-carbon fatty acids (14:0) to 16-carbon species (16:0)
Gene Name:: ELO1
Uniprot ID:: P39540
Molecular weight:: 36233.60156

Reactions

Acyl-CoA + malonyl-CoA → 3-oxoacyl-CoA + CoA + CO(2).

Protein Details

3. Acyl carrier protein, mitochondrial

General function:: Involved in acyl carrier activity
Specific function:: Carrier of the growing fatty acid chain in fatty acid biosynthesis. May be involved in the synthesis of very-long-chain fatty acids. Accessory and non-catalytic subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), which functions in the transfer of electrons from NADH to the respiratory chain
Gene Name:: ACP1
Uniprot ID:: P32463
Molecular weight:: 13942.5

Protein Details

4. Fatty acid synthase subunit beta

General function:: Involved in transferase activity
Specific function:: Fatty acid synthetase catalyzes the formation of long- chain fatty acids from acetyl-CoA, malonyl-CoA and NADPH. The beta subunit contains domains for:[acyl-carrier-protein] acetyltransferase and malonyltransferase, S-acyl fatty acid synthase thioesterase, enoyl-[acyl-carrier-protein] reductase, and 3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase
Gene Name:: FAS1
Uniprot ID:: P07149
Molecular weight:: 228689.0

Reactions

Acetyl-CoA + n malonyl-CoA + 2n NADH + 2n NADPH → long-chain-acyl-CoA + n CoA + n CO(2) + 2n NAD(+) + 2n NADP(+).
Acetyl-CoA + [acyl-carrier-protein] → CoA + acetyl-[acyl-carrier-protein].
Malonyl-CoA + [acyl-carrier-protein] → CoA + malonyl-[acyl-carrier-protein].
(3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] → hexadec-2-enoyl-[acyl-carrier-protein] + H(2)O.
Acyl-[acyl-carrier-protein] + NAD(+) → trans-2,3-dehydroacyl-[acyl-carrier-protein] + NADH.
Oleoyl-[acyl-carrier-protein] + H(2)O → [acyl-carrier-protein] + oleate.

Protein Details

5. Fatty acid synthase subunit alpha

General function:: Involved in magnesium ion binding
Specific function:: Fatty acid synthetase catalyzes the formation of long- chain fatty acids from acetyl-CoA, malonyl-CoA and NADPH. The alpha subunit contains domains for:acyl carrier protein, 3- oxoacyl-[acyl-carrier-protein] reductase, and 3-oxoacyl-[acyl- carrier-protein] synthase. This subunit coordinates the binding of the six beta subunits to the enzyme complex
Gene Name:: FAS2
Uniprot ID:: P19097
Molecular weight:: 206945.0

Reactions

Acetyl-CoA + n malonyl-CoA + 2n NADH + 2n NADPH → long-chain-acyl-CoA + n CoA + n CO(2) + 2n NAD(+) + 2n NADP(+).
Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] → 3-oxoacyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein].
(3R)-3-hydroxyacyl-[acyl-carrier-protein] + NADP(+) → 3-oxoacyl-[acyl-carrier-protein] + NADPH.

Protein Details

6. Acetyl-CoA carboxylase, mitochondrial

General function:: Involved in acetyl-CoA carboxylase activity
Specific function:: Catalyzes the rate-limiting reaction in the mitochondrial fatty acid synthesis (FAS) type II pathway. Responsible for the production of the mitochondrial malonyl-CoA, used for the biosynthesis of the cofactor lipoic acid. This protein carries three functions:biotin carboxyl carrier protein, biotin carboxylase, and carboxyltransferase
Gene Name:: HFA1
Uniprot ID:: P32874
Molecular weight:: 259161.0

Reactions

ATP + acetyl-CoA + HCO(3)(-) → ADP + phosphate + malonyl-CoA.
ATP + biotin-[carboxyl-carrier-protein] + CO(2) → ADP + phosphate + carboxy-biotin-[carboxyl-carrier-protein].

Protein Details

7. Acetyl-CoA carboxylase

General function:: Involved in acetyl-CoA carboxylase activity
Specific function:: Carries out three functions:biotin carboxyl carrier protein, biotin carboxylase and carboxyltransferase
Gene Name:: FAS3
Uniprot ID:: Q00955
Molecular weight:: 250351.0

Reactions

ATP + acetyl-CoA + HCO(3)(-) → ADP + phosphate + malonyl-CoA.
ATP + biotin-[carboxyl-carrier-protein] + CO(2) → ADP + phosphate + carboxy-biotin-[carboxyl-carrier-protein].

Protein Details

8. Malonyl CoA-acyl carrier protein transacylase, mitochondrial

General function:: Involved in transferase activity
Specific function:: Involved in biosynthesis of fatty acids in mitochondria
Gene Name:: MCT1
Uniprot ID:: Q12283
Molecular weight:: 40706.89844

Reactions

Malonyl-CoA + [acyl-carrier-protein] → CoA + malonyl-[acyl-carrier-protein].

Structure for #<Compound:0x05457f18>

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