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Information on EC 6.2.1.76 - malonate-CoA ligase
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6.2.1.76 malonate-CoA ligaseIUBMB Comments
The enzyme, found in mitochondria, detoxifies malonate, which is a potent inhibitor of mitochondrial respiration, and provides malonyl-CoA to the mitochondrial fatty acid biosynthesis pathway.
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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
Synonyms
acsf3, malonyl-coa synthetase, aae13, acyl activating enzyme13, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
AAE13
ACSF3
malonyl-CoA synthetase
AAE13
-
-
-
-
ACSF3
-
-
-
-
malonyl-CoA synthetase
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ATP + malonate + CoA = AMP + diphosphate + malonyl-CoA
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
malonate:CoA ligase (AMP-forming)
The enzyme, found in mitochondria, detoxifies malonate, which is a potent inhibitor of mitochondrial respiration, and provides malonyl-CoA to the mitochondrial fatty acid biosynthesis pathway.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + 2-methylmalonate + CoA
AMP + diphosphate + 2-methyl-malonyl-CoA
-
activity is 53.6% compared to the activity with malonate
-
-
?
ATP + 2-methylmalonate + CoA
AMP + diphosphate + 2-methyl-malonyl-CoA
-
activity is 53.6% compared to the activity with malonate
-
-
?
ATP + 2-methylmalonate + CoA
AMP + diphosphate + 2-methylmalonyl-CoA
activity with 2-methylmalonate is 12% compared to the activity malonate
-
-
?
ATP + 2-methylmalonate + CoA
AMP + diphosphate + 2-methylmalonyl-CoA
activity is 20.4% compared to the activity with malonate
-
-
?
ATP + malonate + CoA
AMP + diphosphate + malonyl-CoA
-
-
-
?
ATP + malonate + CoA
AMP + diphosphate + malonyl-CoA
little or no activity against other dicarboxylic or fatty acids
-
-
?
ATP + malonate + CoA
AMP + diphosphate + malonyl-CoA
-
high substrate specificity on malonate and ATP
-
-
?
ATP + malonate + CoA
AMP + diphosphate + malonyl-CoA
ordered bi uni uni bi ping pong ter ter mechanism
-
-
?
ATP + malonate + CoA
AMP + diphosphate + malonyl-CoA
-
-
-
-
?
ATP + malonate + CoA
AMP + diphosphate + malonyl-CoA
-
high substrate specificity on malonate and ATP
-
-
?
ATP + malonate + CoA
AMP + diphosphate + malonyl-CoA
-
-
-
?
ATP + malonate + CoA
AMP + diphosphate + malonyl-CoA
no activity with oxalate, succinate, butyrate, octanoate, laurate, palmitate, oleate, or lignocerate
-
-
?
ATP + malonate + CoA
AMP + diphosphate + malonyl-CoA
-
-
-
?
ATP + malonate + CoA
AMP + diphosphate + malonyl-CoA
with activity with acetate, propionate, or succinate in place of malonate, or with GTP or CTP in place of ATP
-
-
?
ATP + methylmalonate + CoA
AMP + diphosphate + methylmalonyl-CoA
70.3% of the activity compared to malonate
-
-
?
ATP + methylmalonate + CoA
AMP + diphosphate + methylmalonyl-CoA
the kcat/KM value for methylmalonate is 12.6fold lower than the kcat/Km value for malonate
-
-
?
additional information
?
-
no activity for acetate, propionate and succinate in place of malonate, and for GTP, CTP and AMP in place of ATP
-
-
-
additional information
?
-
-
no activity for acetate, propionate and succinate in place of malonate, and for GTP, CTP and AMP in place of ATP
-
-
-
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + malonate + CoA
AMP + diphosphate + malonyl-CoA
-
-
-
?
ATP + malonate + CoA
AMP + diphosphate + malonyl-CoA
-
-
-
-
?
ATP + malonate + CoA
AMP + diphosphate + malonyl-CoA
-
-
-
?
ATP + malonate + CoA
AMP + diphosphate + malonyl-CoA
-
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
glycerol
-
when the glycerol content in the assay mixture was 1.24-3.24% (v/v), enzyme activity is highest. Increased or decreased glycerol content gradually decreases activity
pyridoxal-5'-phosphate
-
3 mM, 15 min, almost complete loss of activity
additional information
-
no inhibition: iodoacetamide or p-chloromercuriphenylsulphonate
-
diethylpyrocarbonate
-
2 mM, 7 min, almost complete loss of activity
diethylpyrocarbonate
-
the enzyme is inactivated by diethylpyrocarbonate with the second-order rate constant of 775/M*min at pH 7.0, 25°C
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.02
ATP
pH 7.0, 30°C, wild-type enzyme, cosubstrate: methylmalonate
0.0338
ATP
pH and temperature not specified in the publication
0.052
ATP
pH 7.0, 30°C, wild-type enzyme, cosubstrate: malonate
0.058
ATP
pH 7.0, 30°C, mutant enzyme R168G, cosubstrate: methylmalonate
0.059
ATP
pH 7.0, 30°C, mutant enzyme H206L, cosubstrate: malonate
0.063
ATP
pH 7.0, 30°C, mutant enzyme R168G, cosubstrate: malonate
0.072
ATP
pH 7.0, 30°C, mutant enzyme K170M, cosubstrate: methylmalonate
0.076
ATP
pH 7.0, 30°C, mutant enzyme K170M, cosubstrate: malonate
0.106
ATP
pH 7.0, 30°C, mutant enzyme R168G/K170M, cosubstrate: malonate
0.0078
CoA
pH 7.0, 30°C, mutant enzyme H206L, cosubstrate: malonate
0.0078
CoA
pH 7.0, 30°C, mutant enzyme K170M, cosubstrate: methylmalonate
0.0081
CoA
pH 7.0, 30°C, wild-type enzyme, cosubstrate: methylmalonate
0.017
CoA
pH 7.0, 30°C, mutant enzyme R168G, cosubstrate: methylmalonate
0.0267
CoA
pH and temperature not specified in the publication
0.046
CoA
pH 7.0, 30°C, wild-type enzyme, cosubstrate: malonate
0.054
CoA
pH 7.0, 30°C, mutant enzyme K170M, cosubstrate: malonate
0.074
CoA
pH 7.0, 30°C, mutant enzyme R168G/K170M, cosubstrate: malonate
0.133
CoA
pH 7.0, 30°C, mutant enzyme R168G, cosubstrate: malonate
0.113
malonate
pH and temperature not specified in the publication
0.529
malonate
pH 7.5, temperature not specified in the publication
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.38
ATP
pH 7.0, 30°C, mutant enzyme H206L, cosubstrate: malonate
0.6
ATP
pH 7.0, 30°C, mutant enzyme K170M, cosubstrate: methylmalonate
2.7
ATP
pH 7.0, 30°C, wild-type enzyme, cosubstrate: methylmalonate
2.9
ATP
pH 7.0, 30°C, mutant enzyme R168G/K170M, cosubstrate: malonate
3
ATP
pH 7.0, 30°C, mutant enzyme R168G, cosubstrate: methylmalonate
9
ATP
pH 7.0, 30°C, mutant enzyme K170M, cosubstrate: malonate
12
ATP
pH 7.0, 30°C, mutant enzyme R168G, cosubstrate: malonate
0.55
CoA
pH 7.0, 30°C, mutant enzyme H206L, cosubstrate: malonate
0.56
CoA
pH 7.0, 30°C, mutant enzyme K170M, cosubstrate: methylmalonate
3.1
CoA
pH 7.0, 30°C, mutant enzyme R168G, cosubstrate: methylmalonate
3.2
CoA
pH 7.0, 30°C, mutant enzyme R168G/K170M, cosubstrate: malonate
3.3
CoA
pH 7.0, 30°C, wild-type enzyme, cosubstrate: methylmalonate
9.2
CoA
pH 7.0, 30°C, mutant enzyme K170M, cosubstrate: malonate
13
CoA
pH 7.0, 30°C, mutant enzyme R168G, cosubstrate: malonate
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
6.4
ATP
pH 7.0, 30°C, mutant enzyme H206L, cosubstrate: malonate
8.3
ATP
pH 7.0, 30°C, mutant enzyme K170M, cosubstrate: methylmalonate
27
ATP
pH 7.0, 30°C, mutant enzyme R168G/K170M, cosubstrate: malonate
52
ATP
pH 7.0, 30°C, mutant enzyme R168G, cosubstrate: methylmalonate
118
ATP
pH 7.0, 30°C, mutant enzyme K170M, cosubstrate: malonate
135
ATP
pH 7.0, 30°C, wild-type enzyme, cosubstrate: methylmalonate
190
ATP
pH 7.0, 30°C, mutant enzyme R168G, cosubstrate: malonate
43
CoA
pH 7.0, 30°C, mutant enzyme R168G/K170M, cosubstrate: malonate
71
CoA
pH 7.0, 30°C, mutant enzyme H206L, cosubstrate: malonate
72
CoA
pH 7.0, 30°C, mutant enzyme K170M, cosubstrate: methylmalonate
98
CoA
pH 7.0, 30°C, mutant enzyme R168G, cosubstrate: malonate
170
CoA
pH 7.0, 30°C, mutant enzyme K170M, cosubstrate: malonate
182
CoA
pH 7.0, 30°C, mutant enzyme R168G, cosubstrate: methylmalonate
407
CoA
pH 7.0, 30°C, wild-type enzyme, cosubstrate: methylmalonate
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
highest levels is found in brown adipose tissue, kidney, and liver
brenda
highest levels is found in brown adipose tissue, kidney, and liver
brenda
highest levels is found in brown adipose tissue, kidney, and liver
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
human ACSF3 is located exclusively in mitochondria
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
metabolism
physiological function
malfunction
aae13 null mutants grow poorly and accumulated malonic and succinic acids
malfunction
loss of ACSF3 perturbs mitochondrial metabolism. Impaired mitochondrial malonate metabolism affects cellular energy status and impairs de novo lipogenesis
metabolism
a major role for ACSF3 is to provide a metabolic pathway for the clearance of malonate by the generation of malonyl-CoA, which can then be decarboxylated to acetyl-CoA by malonyl-CoA decarboxylase. Additionally, ACSF3-derived malonyl-CoA can be used to malonylate lysine residues on proteins within the matrix of mitochondria, possibly adding another regulatory layer to post-translational control of mitochondrial metabolism
metabolism
overexpression of a malonyl-CoA synthetase leads to significant increase in both lipid and polyketide accumulation. AAE13 expression increases lipid accumulation. Overexpression of AAE13 leads to significant increases in resveratrol accumulation. Overexpression of AAE13 suppresses the TCA cycle in transgenic yeast
physiological function
AAE13 is required to metabolize free malonate and prevent its accumulation to levels that are toxic to cell metabolism and plant growth
physiological function
ACSF3 is involved in the formation of the malonyl-ACP moieties required as substrates for the mitochondrial de novo fatty acid synthesis pathway
physiological function
essential role for the enzyme (ACSF3) in dictating the metabolic fate of mitochondrial malonate and malonyl-CoA in mammalian metabolism. ACSF3 is required for the metabolism and therefore detoxification of malonate, ACSF3-derived malonyl-CoA is specifically required for lysine malonylation of mitochondrial proteins
physiological function
whereas the cytosolic AAE13 protein is not essential, due to the presence of a redundant malonyl-CoA generating system provided by a cytosolic acetyl-CoA carboxylase, the mitochondrial AAE13 protein is essential for plant growth
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
R354A
the mutant enzyme is completely devoid of malonyl-CoA synthetase activity, although the Ala354 mutant retains the same very low activity toward acetate that is observed with the wild-type enzyme
R354L
the mutant enzyme is completely devoid of malonyl-CoA synthetase activity
K170M
R168G
R168G/K170M
R168G
kcat value for malonyl-CoA formation is reduced 1.7fold. The mutant enzyme shows slightly higher methyl malonyl-CoA synthetase activity than the wild type
R168G/K170M
kcat value for malonyl-CoA formation is reduced 6.1fold
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
50
-
the enzyme loses 80% of activity within 30 min. When ATP and malonate are added to the enzyme solution, activity loss is reduced down to 50%
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4°C, purified enzyme in 20 mM-phosphate buffer (pH 6.9), 15% glycerol, no detectable loss of activity after several months
-
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Bowman, C.E.; Wolfgang, M.J.
Role of the malonyl-CoA synthetase ACSF3 in mitochondrial metabolism
Adv. Biol. Regul.
71
34-40
2019
Homo sapiens (Q4G176)
brenda
Wang, Y.; Chen, H.; Yu, O.
A plant malonyl-CoA synthetase enhances lipid content and polyketide yield in yeast cells
Appl. Microbiol. Biotechnol.
98
5435-5447
2014
Arabidopsis thaliana (Q8H151)
brenda
Kim, Y.S.; Chae, H.Z.
Purification and properties of malonyl-CoA synthetase from Rhizobium japonicum
Biochem. J.
273
511-516
1991
Bradyrhizobium japonicum, Bradyrhizobium japonicum USDA 110
brenda
Kim, Y.S.; Kang, S.W.
Steady-state kinetics of malonyl-CoA synthetase from Bradyrhizobium japonicum and evidence for malonyl-AMP formation in the reaction
Biochem. J.
297
327-333
1994
Bradyrhizobium japonicum (Q9LAR4), Bradyrhizobium japonicum
brenda
An, J.H.; Lee, G.Y.; Jung, J.W.; Lee, W.; Kim, Y.S.
Identification of residues essential for a two-step reaction by malonyl-CoA synthetase from Rhizobium trifolii
Biochem. J.
344
159-166
1999
Rhizobium leguminosarum (Q9ZIP5), Rhizobium leguminosarum
brenda
Bowman, C.E.; Rodriguez, S.; Selen Alpergin, E.S.; Acoba, M.G.; Zhao, L.; Hartung, T.; Claypool, S.M.; Watkins, P.A.; Wolfgang, M.J.
The mammalian malonyl-CoA synthetase ACSF3 is required for mitochondrial protein malonylation and metabolic efficiency
Cell Chem. Biol.
24
673-684.e4
2017
Homo sapiens (Q4G176)
brenda
An, J.H.; Kim, Y.S.
A gene cluster encoding malonyl-CoA decarboxylase (MatA), malonyl-CoA synthetase (MatB) and a putative dicarboxylate carrier protein (MatC) in Rhizobium trifolii--cloning, sequencing, and expression of the enzymes in Escherichia coli
Eur. J. Biochem.
257
395-402
1998
Rhizobium leguminosarum (Q9ZIP5), Rhizobium leguminosarum
brenda
Gueguen, V.; Macherel, D.; Jaquinod, M.; Douce, R.; Bourguignon, J.
Fatty acid and lipoic acid biosynthesis in higher plant mitochondria
J. Biol. Chem.
275
5016-5025
2000
Pisum sativum
brenda
Witkowski, A.; Thweatt, J.; Smith, S.
Mammalian ACSF3 protein is a malonyl-CoA synthetase that supplies the chain extender units for mitochondrial fatty acid synthesis
J. Biol. Chem.
286
33729-33736
2011
Mus musculus (Q3URE1), Homo sapiens (Q4G176), Homo sapiens
brenda
Kim, Y.S.; Kim, Y.I.; Bang, S.K.
Chemical modification of Pseudomonas fluorescens malonyl-CoA synthetase by diethylpyrocarbonate kinetic evidence for an essential histidyl residue on alpha subunit
J. Protein Chem.
10
407-413
1991
Pseudomonas fluorescens
brenda
Chen, H.; Kim, H.U.; Weng, H.; Browse, J.
Malonyl-CoA synthetase, encoded by ACYL ACTIVATING ENZYME13, is essential for growth and development of Arabidopsis
Plant Cell
23
2247-2262
2011
Homo sapiens (Q4G176), Arabidopsis thaliana (Q8H151), Arabidopsis thaliana
brenda
Guan, X.; Nikolau, B.J.
AAE13 encodes a dual-localized malonyl-CoA synthetase that is crucial for mitochondrial fatty acid biosynthesis
Plant J.
85
581-593
2016
Arabidopsis thaliana (Q8H151)
brenda
Jung, J.W.; An, J.H.; Na, K.B.; Kim, Y.S.; Lee, W.
The active site and substrates binding mode of malonyl-CoA synthetase determined by transferred nuclear Overhauser effect spectroscopy, site-directed mutagenesis, and comparative modeling studies
Protein Sci.
9
1294-1303
2000
Rhizobium leguminosarum (Q9ZIP5), Rhizobium leguminosarum
brenda
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