Record Information
Version2.0
Creation Date2012-05-31 13:46:53 -0600
Update Date2015-09-17 15:41:10 -0600
Secondary Accession Numbers
  • ECMDB01175
Identification
Name:Malonyl-CoA
Description:Malonyl-CoA is a coenzyme A derivative which plays a key role in fatty acid synthesis in E. coli Fatty acids must be activated with CoA before any chemical modification can be applied. Also fatty acid metabolic intermediates will also exists as CoA derivatives until the CoA is enzymatically cleaved. The fatty acid group is linked to the terminal thiol moiety of CoA
Structure
Thumb
Synonyms:
  • Malonyl CoA
  • Malonyl Coenzyme A
  • Malonyl-CoA
  • Malonyl-Coenzyme A
  • MalonylCoenzyme 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
  • S-(Hydrogen propanedioic acid) CoA
  • S-(Hydrogen propanedioic acid) coenzyme A
Chemical Formula:C24H38N7O19P3S
Weight:Average: 853.58
Monoisotopic: 853.115602295
InChI Key:LTYOQGRJFJAKNA-VFLPNFFSSA-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
CAS number:524-14-1
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
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(O)C(=O)NCCC(=O)NCCSC(=O)CC(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
  • Aminopyrimidine
  • Imidolactam
  • Alkyl phosphate
  • 1,3-dicarbonyl compound
  • Pyrimidine
  • Primary aromatic amine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • N-substituted imidazole
  • Monosaccharide
  • 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
State:Solid
Charge:-5
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility3.8 g/LALOGPS
logP-0.62ALOGPS
logP-7.1ChemAxon
logS-2.4ALOGPS
pKa (Strongest Acidic)0.82ChemAxon
pKa (Strongest Basic)4.97ChemAxon
Physiological Charge-5ChemAxon
Hydrogen Acceptor Count19ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area400.93 ŲChemAxon
Rotatable Bond Count22ChemAxon
Refractivity178.55 m³·mol⁻¹ChemAxon
Polarizability74.68 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
Acetyl-CoA + Adenosine triphosphate + Hydrogen carbonate <> ADP + Hydrogen ion + Malonyl-CoA + Phosphate
acyl carrier protein + Malonyl-CoA <> Coenzyme A + Malonyl-[acyl-carrier protein]
S-Adenosylmethionine + Malonyl-CoA > S-Adenosylhomocysteine + malonyl-CoA methyl ester
Adenosine triphosphate + Acetyl-CoA + Hydrogen carbonate <> ADP + Phosphate + Malonyl-CoA
Malonyl-CoA + Acyl-carrier protein + Acyl-carrier protein <> Coenzyme A + Malonyl-[acyl-carrier protein] + Malonyl-[acyl-carrier protein]
Acetyl-CoA + Carboxybiotin-carboxyl-carrier protein <> Malonyl-CoA + Holo-[carboxylase]
Adenosine triphosphate + Acetyl-CoA + Hydrogen carbonate > Hydrogen ion + Malonyl-CoA + Phosphate + ADP
Malonyl-CoA + S-Adenosylmethionine > malonyl-CoA methyl ester + S-Adenosylhomocysteine
Adenosine triphosphate + Acetyl-CoA + Carbonic acid > ADP + Inorganic phosphate + Malonyl-CoA
Adenosine triphosphate + Acetyl-CoA + Carbonic acid > ADP + Inorganic phosphate + Malonyl-CoA
Adenosine triphosphate + Acetyl-CoA + Carbonic acid > ADP + Inorganic phosphate + Malonyl-CoA
S-adenosyl-L-methionine + Malonyl-CoA > S-Adenosylhomocysteine + malonyl-CoA methyl ester
Malonyl-CoA + [acyl-carrier-protein] > CoA + malonyl-[acyl-carrier-protein]
Acetyl-CoA + Hydrogen carbonate + Adenosine triphosphate > Adenosine diphosphate + Phosphate + Hydrogen ion + Malonyl-CoA + ADP + Malonyl-CoA
Malonyl-CoA + a holo-[acyl-carrier protein]  + Malonyl-CoA > Coenzyme A + a malonyl-[acp]
Malonyl-CoA + a holo-[acyl-carrier protein] + Malonyl-CoA > Coenzyme A + a malonyl-[acp]
a biotinylated [BCCP dimer] + Hydrogen ion + Phosphate + ADP + Malonyl-CoA < Water + Acetyl-CoA + Adenosine triphosphate + carboxylated-biotinylated [BCCP dimer]
SMPDB Pathways:
Fatty acid biosynthesisPW000900 ThumbThumb?image type=greyscaleThumb?image type=simple
Phenylalanine metabolismPW000921 ThumbThumb?image type=greyscaleThumb?image type=simple
Propanoate metabolismPW000940 ThumbThumb?image type=greyscaleThumb?image type=simple
beta-Alanine metabolismPW000896 ThumbThumb?image type=greyscaleThumb?image type=simple
biotin-carboxyl carrier protein assemblyPW002067 ThumbThumb?image type=greyscaleThumb?image type=simple
fatty acid elongation -- saturatedPW000798 ThumbThumb?image type=greyscaleThumb?image type=simple
palmitate biosynthesisPW000797 ThumbThumb?image type=greyscaleThumb?image type=simple
palmitate biosynthesis 2PW002044 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
  • 7-keto-8-aminopelargonate biosynthesis I PWY-6519
  • biotin-carboxyl carrier protein assembly PWY0-1264
  • fatty acid biosynthesis initiation I PWY-4381
Concentrations
ConcentrationStrainMediaGrowth StatusGrowth SystemTemperatureDetails
35± 0 uMK12 NCM3722Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glucoseMid-Log PhaseShake flask and filter culture37 oCPMID: 19561621
Find out more about how we convert literature concentrations.
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-1912000130-da8095652669b99c8349View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0913000000-c93bc8aa729d6712ed08View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-2911000000-dee360a0ee5e683d782cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001i-9830140570-8e78a24b9858f67c1579View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-5910010010-97fdf25aafbfdff7c908View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-057i-6900100000-33483ed329c67d3c4cacView in MoNA
References
References:
  • Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. Pubmed: 19561621
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
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.
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID15531
HMDB IDHMDB01175
Pubchem Compound ID10663
Kegg IDC00083
ChemSpider ID10213
WikipediaMalonyl-CoA
BioCyc IDMALONYL-COA
EcoCyc IDMALONYL-COA
Ligand ExpoMLC

Enzymes

General function:
Involved in acetyl-CoA carboxylase activity
Specific function:
Controls translation of mRNA for both itself and the alpha-subunit (accA) by binding to a probable hairpin in the 5' of the mRNA. Binding to mRNA inhibits translation; this is partially relieved by acetyl-CoA. Increasing amounts of mRNA also inhibit enzyme activity
Gene Name:
accD
Uniprot ID:
P0A9Q5
Molecular weight:
33322
Reactions
ATP + acetyl-CoA + HCO(3)(-) = ADP + phosphate + malonyl-CoA.
General function:
Involved in transferase activity
Specific function:
Malonyl-CoA + [acyl-carrier-protein] = CoA + malonyl-[acyl-carrier-protein]
Gene Name:
fabD
Uniprot ID:
P0AAI9
Molecular weight:
32417
Reactions
Malonyl-CoA + [acyl-carrier-protein] = CoA + malonyl-[acyl-carrier-protein].
General function:
Involved in acetyl-CoA carboxylase activity
Specific function:
Component of the acetyl coenzyme A carboxylase (ACC) complex. First, biotin carboxylase catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the carboxyltransferase to acetyl-CoA to form malonyl-CoA
Gene Name:
accA
Uniprot ID:
P0ABD5
Molecular weight:
35241
Reactions
ATP + acetyl-CoA + HCO(3)(-) = ADP + phosphate + malonyl-CoA.
General function:
Involved in acetyl-CoA carboxylase activity
Specific function:
This protein is a component of the acetyl coenzyme A carboxylase complex; first, biotin carboxylase catalyzes the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-CoA
Gene Name:
accB
Uniprot ID:
P0ABD8
Molecular weight:
16687
General function:
Involved in ligase activity
Specific function:
This protein is a component of the acetyl coenzyme A carboxylase complex; first, biotin carboxylase catalyzes the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-CoA
Gene Name:
accC
Uniprot ID:
P24182
Molecular weight:
49320
Reactions
ATP + biotin-[carboxyl-carrier-protein] + CO(2) = ADP + phosphate + carboxy-biotin-[carboxyl-carrier-protein].
ATP + acetyl-CoA + HCO(3)(-) = ADP + phosphate + malonyl-CoA.
General function:
Involved in biotin biosynthetic process
Specific function:
BioC is involved in an early, but chemically unexplored, step in the conversion of pimelic acid to biotin
Gene Name:
bioC
Uniprot ID:
P12999
Molecular weight:
28276
Reactions
S-adenosyl-L-methionine + malonyl-CoA = S-adenosyl-L-homocysteine + malonyl-CoA methyl ester.
General function:
Involved in fatty acid biosynthetic process
Specific function:
Carrier of the growing fatty acid chain in fatty acid biosynthesis
Gene Name:
acpP
Uniprot ID:
P0A6A8
Molecular weight:
8640