Information on EC 2.3.3.9 - malate synthase

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea

EC NUMBER
COMMENTARY hide
2.3.3.9
-
RECOMMENDED NAME
GeneOntology No.
malate synthase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
acetyl-CoA + glyoxylate + H2O = (S)-malate + CoA
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
aldol condensation
-
-
-
-
Claisen condensation
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Biosynthesis of secondary metabolites
-
-
chitin degradation to ethanol
-
-
citric acid cycle
-
-
glycolate and glyoxylate degradation II
-
-
Glyoxylate and dicarboxylate metabolism
-
-
glyoxylate cycle
-
-
L-arabinose degradation IV
-
-
Metabolic pathways
-
-
methylaspartate cycle
-
-
Microbial metabolism in diverse environments
-
-
Pyruvate metabolism
-
-
TCA cycle IV (2-oxoglutarate decarboxylase)
-
-
TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase)
-
-
xylose degradation IV
-
-
SYSTEMATIC NAME
IUBMB Comments
acetyl-CoA:glyoxylate C-acetyltransferase (thioester-hydrolysing, carboxymethyl-forming)
The enzyme catalyses the irreversible condensation of acetyl-CoA with glyoxylate to form (S)-malate. Among other functions, the enzyme participates in the glyoxylate cycle, a modified version of the TCA cycle that bypasses steps that lead to a loss of CO2.
CAS REGISTRY NUMBER
COMMENTARY hide
9013-48-3
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
B0Q556
Uniprot
Manually annotated by BRENDA team
thermophilic
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
pK 233
-
-
Manually annotated by BRENDA team
Candida tropicalis pK 233
pK 233
-
-
Manually annotated by BRENDA team
induced by growth on acetate and light
Swissprot
Manually annotated by BRENDA team
formerly Vibrio sp. strain ABE-1
-
-
Manually annotated by BRENDA team
Cucurbita sp.
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
sunflower
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
ssp. indica cv Guangluai 4
-
-
Manually annotated by BRENDA team
strain Pb01
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
NRRL3585
SwissProt
Manually annotated by BRENDA team
NRRL3585
SwissProt
Manually annotated by BRENDA team
expression with GST-tag in Escherichia coli
Swissprot
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
acetyl-CoA + glyoxylate + H2O
(S)-malate + CoA
show the reaction diagram
acetyl-CoA + glyoxylate + H2O
CoA + (S)-malate
show the reaction diagram
acetyl-CoA + H2O + glyoxylate
(S)-malate + CoA
show the reaction diagram
glyoxylate + acetyl-CoA + H2O
(S)-malate + CoA
show the reaction diagram
glyoxylate + butyryl-CoA + H2O
2-oxohexanedioic acid + CoA
show the reaction diagram
-
-
-
-
ir
glyoxylate + fluoroacetyl-CoA + H2O
2-oxo-3-fluoro-butanedioic acid + CoA
show the reaction diagram
-
-
-
-
ir
glyoxylate + propionyl-CoA + H2O
2-oxopentanedioic acid + CoA
show the reaction diagram
-
-
-
-
ir
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
acetyl-CoA + H2O + glyoxylate
(S)-malate + CoA
show the reaction diagram
glyoxylate + acetyl-CoA + H2O
(S)-malate + CoA
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ba2+
-
about 30% of the activation with Mg2+
KCl
-
salt optimum: 3.0 M KCl
Ni2+
-
about 98% of the activation with Mg2+
additional information
-
Co2+, Fe2+, Ca2+, Ba2+, Ni2+, Cd2+, Zn2+, Cu2+, Hg2+ are not able to support the activity of enzyme
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2,4,5-trioxopyrrolidine-3-carboxamide
-
; competitive
acetaldehyde
-
weak
acetyl-CoA
Butanedione
-
slight inhibition at high concentrations
Ca2+
-
5 mM, 19% residual activity
Chloroacetyl-CoA
-
-
citrate
-
1 mM, 82% residual activity
coenzyme A
-
0.1 mM, 56% residual activity
D-fructose-1,6-bisphosphate
-
10 mM, 60% residual activity
deamino-acetyl-CoA
-
-
deoxycholate
-
-
dephosphoacetyl-CoA
-
-
dethio-CoA
uncompetitive inhibitor versus glyoxylate and competitive inhibitor versus acetyl-CoA
diethyl dicarbonate
-
inhibition prevented by preincubation with acetyl-CoA
EDTA
-
1.0 mM, 30% inhibition
fluoroacetate
glycolate
Glyoxal
-
10 mM, 70% residual activity
glyoxylate
iodoacetate
-
5 mM, 6% residual activity
K+
-
5 mM, 5% residual activity
malate
-
1.0 mM, 50% inhibition
methylglyoxal
-
-
Mn2+
-
5 mM, 16% residual activity
Na+
-
5 mM, 10% residual activity
oxalate
oxaloacetate
p-chloromercuribenzoate
-
0.05 mM, 9% residual activity
parabanic acid
-
; competitive
phosphoenolpyruvate
pyridoxal-5'-phosphate
-
preincubation with glyoxylate but not acetyl-CoA prevents inhibition
pyruvate
S-Acetonyl-CoA
-
-
S-Ethyl-CoA
-
-
additional information
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
EDTA
-
0.01 mM, 10% activation
Triton X-100
-
activation
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00012 - 0.11
acetyl-CoA
0.045
glyoxalate
-
pH 8.0, 30C
0.00011 - 2
glyoxylate
additional information
additional information
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
23 - 161
acetyl-CoA
3.19 - 48.1
glyoxylate
additional information
additional information
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.04 - 0.113
2,4,5-trioxopyrrolidine-3-carboxamide
0.01 - 4.3
ATP
0.06
Bromopyruvate
-
-
0.246
fluoroacetate
0.07 - 0.9
glycolate
0.019 - 1.5
oxalate
1.5
oxaloacetate
-
-
0.37 - 0.55
parabanic acid
0.2
phosphoenolpyruvate
-
-
0.54 - 1.6
pyruvate
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
pyruvate
Pseudomonas aeruginosa
-
1 mM pyruvate: 40% activity
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
2.39
-
mutant R338K, pH 8.0, 37C
3.73
cells grown in the presence of potassium acetate
5.19
30C, pH 8.0
6
-
recombinant enzyme
15.6
mutant D453A, pH 7.9
24.5
-
-
26.9
-
wild-type enzyme
27
-
mutant enzyme PC2 NG35
31.8
-
mutant C617S, pH 8.0, 37C
36.1
-
wild-type, pH 8.0, 37C
44.2
mutant R171L, pH 7.9
25090
wild-type, pH 7.9
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8
-
assay at
8.2
-
phosphate-citrate-borate buffer or MOPS-KOH buffer
additional information
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 9.5
-
pH 5.0: about 35% of maximal activity, pH 9.5: about 70% of maximal activity
6.8 - 9.7
-
pH 6.8 and 9.7: about 50% of maximal activity, phosphate-citrate-borate buffer
7 - 10
-
pH 7.0: about 40% of maximal activity, pH 10.0: about 45% of maximal activity
7 - 8.5
-
pH 7.0: about 80% of maximal activity, pH 8.7: about 60% of maximal activity, enzyme form MSL and MSH
7
-
87% activity
7.5 - 8.5
malate synthase reaction
7.5 - 10.5
-
pH 7.5: about 55% of maximal activity, pH 10.5: about 25% of maximal activity, enzyme form MSL and MSH
8 - 10
10
-
85% activity
additional information
-
below pH 6: no activity remains, outside pH 7-10 the activity decreases rapidly
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5
-
15.5% activity
15
-
47.1% activity
20 - 45
25 - 80
-
25C: about 45% of maximal activity, 80C: about 45% of maximal activity
32.5 - 40
-
more than 90% of activity
additional information
-
Km for glyoxylate increases with decreasing temperature
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
-
abundant in ehtanol-grown cells
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2)
Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2)
Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2)
Mycobacterium leprae (strain Br4923)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
52000 - 54000
-
gel filtration, equilibrum sedimentation centrifugation, light scattering, two distinct forms of enzyme
55000
-
gel filtration
65000
-
gel filtration, enzyme form MSL
110000
-
gel filtration
120000
Cucurbita sp.
-
sucrose density gradient centrifugation
160000
170000
-
gel filtration, ultracentrifugation, sucrose density gradient centrifugation
180000
-
high speed equilibrium sedimentation
186000
-
small-angle X-ray scattering technique
200000
-
gel filtration
250000
350000
-
gel filtation
420000
gel filtration
480000
Cucurbita sp.
-
sucrose density gradient centrifugation
510000
-
gel filtration
520000
575000
-
sucrose density gradient centrifugation
630000
730000
-
gel filtration
750000
-
sucrose density gradient centrifugation
additional information
-
by incubation with 5 mM ATP the high molecular weight enzyme form MSH is converted to the low molecular weight enzyme form MSL
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
decamer
-
10 * 62000, SDS-PAGE
dodecamer
-
12 * 63000, SDS-PAGE
homodimer
homotrimer
monomer
multimer
-
x * 65000
octamer
tetramer
trimer
-
3 * 66000, SDS-PAGE
trimer or hexamer
malate synthase isoform H is found in the native state as a trimer/hexamer equilibrium
additional information
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
no modification
side-chain modification
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
isoform G in complex with Mg2+, pyruvate, and acetyl-CoA
-
structure of enzyme based on a beta8/alpha8 barrel fold
-
malate synthase isoform H in complex with glyoxylate and also as a ternary complex with acetyl-coenzyme A and pyruvate, sitting drop vapor diffusion method, using 0.17 M ammonium acetate, 24.5-27% (w/v) PEG 4500, 15% (v/v) glycerol, and 0.085 M sodium acetate trihydrate at a pH of 4.4-5.0
mixed alpha/beta structure
-
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
1 - 2
-
1 h preincubation: about 5% activity
702873
5
-
1 h preincubation: about 5% activity
702873
5.5
-
4C, 12 h, about 60% loss of activity, enzyme form MSH
638472
6
-
4C, 12 h, about 90% loss of activity, enzyme form MSH
638472
6 - 7
-
1 h preincubation: 100% activity
702873
7 - 8
-
4C, 12 h, stable, enzyme forms MSL and MSH
638472
7
-
inactive at pH 7.0 and below
638491
9
-
4C, 12 h, about 50% loss of activity, enzyme form MSL, about 40% loss of activity of enzyme form MSH
638472
11
-
1 h preincubation: 90% activity
702873
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
-
pH 7.6, 5 min, enzyme form MSL is stable up to
41
-
1 h, little effect
44
-
1 h, complete inactivation
65
-
2 min, 84% loss of activity
70
-
1 h preincubation: complete loss of activity
additional information
-
heating for 3 min, complete inactivation of enzyme form MSL and 65% loss of activity of enzyme form MSH, slight increase of heat stability in presence of glyoxylate and/or Mg2+
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
DTT and glycerol stabilize
-
DTT stabilizes
-
freezing and thawing inactivates
inactivation in air-saturated aqueous solution by X-irradiation, inactivation is mainly due to the action of OH radicals, to a minor extent to O2 radicals and H2O2
-
limited proteolysis with trypsin results in cleavage of malate synthase into two framents of respectively 45000 Da and 19000 Da
-
Mg2+ stabilizes
salt does not stabilize
-
trypsin, treatment for 10 min, about 50% loss of activity of enzyme form MSH, 92% loss of activity of enzyme form MSL
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, stable for more than one month
-
-70C, 200 mM Hepes buffer, containing 6 mM MgCl2, 2 mM 2-mercaptoethanol, pH 7.6, stable for several months
-
-70C, stable for at least 3 months
-
0-4C, stable for at least 2 weeks
-
2C, stable for at least a month
4C, stable for more than 3 weeks
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
DEAE Sepharose column chromatography, HisTrap HP column chromatography, and Superdex 200 pg gel filtration
-
glutathione affinity chromatography, proteolytic removal of the GST tag, anion exchange chromatography
-
Ni-chelate affinity chromatography, His-, Trx-, and S-tag removed by cleavage with enterokinase
Ni-NTA agarose column chromatography and Superdex 200 gel filtration
recombinant enzyme
-
recombinant enzymes
reverse phase chromatography, anion-exchange column chromatography, and gel filtration
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli T7 Express cells
expression in Escherichia coli
expression in Escherichia coli and Corynebacterium glutamicum
GST-tagged version expressed in Escherichia coli
-
His-tag version expressed in Escherichia coli
-
His-tagged version expressed in Escherichia coli
His-tagged version, gene synthesized commercially, expressed in Escherichia coli
B0Q556
overexpressed in Ashbya gossypii
-
wild type enzyme is expressed in Escherichia coli BL21(DE3) cells, mutant enzymes are expressed in Escherichia coli ArcticExpress(DE3) RP cells
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
decrease in transcription after germination, increase of activity after germination
-
during growth on acetate
during infection of tomato plants
-
in the presence of macrophages
regulation by carbon and nitrogen sources, highly induced by oxalurate in the presence of glucose and by proline
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C438S
-
residue in the acetyl-CoA binding pocket
D475N
-
the glyoxylate cycle enzyme mutant completely loses malate synthase activity but retains isocitrate lyase activity
R187K
-
the glyoxylate cycle enzyme mutant completely loses malate synthase activity but retains isocitrate lyase activity
D453A
0.06% of wild-type activity
P186R
-
more thermostable and thermoactive than wild-type
R171L
0.2% of wild-type activity, reduced expression at room temperature, expression of soluble protein at 15C
T8P/L9P
-
more thermostable than wild-type
T8P/L9P/P186R
-
more thermostable and thermoactive than wild-type
D453A
-
0.06% of wild-type activity
-
R171L
-
0.2% of wild-type activity, reduced expression at room temperature, expression of soluble protein at 15C
-
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
agriculture
-
enzyme is required for pathogenicity of the fungal phytopathogen
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