Information on EC 1.1.1.39 - malate dehydrogenase (decarboxylating)

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

EC NUMBER
COMMENTARY hide
1.1.1.39
-
RECOMMENDED NAME
GeneOntology No.
malate dehydrogenase (decarboxylating)
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(S)-malate + NAD+ = pyruvate + CO2 + NADH
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
-
-
-
-
oxidative decarboxylation
-
-
-
-
redox reaction
-
-
-
-
reduction
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
C4 and CAM-carbon fixation
-
-
Pyruvate metabolism
-
-
Carbon fixation in photosynthetic organisms
-
-
Metabolic pathways
-
-
Microbial metabolism in diverse environments
-
-
anaerobic energy metabolism (invertebrates, mitochondrial)
-
-
gluconeogenesis I
-
-
L-malate degradation II
-
-
C4 photosynthetic carbon assimilation cycle, NAD-ME type
-
-
chitin degradation to ethanol
-
-
L-carnitine degradation III
-
-
SYSTEMATIC NAME
IUBMB Comments
(S)-malate:NAD+ oxidoreductase (decarboxylating)
Does not decarboxylate added oxaloacetate.
CAS REGISTRY NUMBER
COMMENTARY hide
9028-46-0
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Amaranthus edulis
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
gene azc3656
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain IFO 13182
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Crassula argentea
-
-
-
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
Heliocarpus sp.
-
-
-
Manually annotated by BRENDA team
gene maeE
-
-
Manually annotated by BRENDA team
Mnium undulatum
-
-
-
Manually annotated by BRENDA team
Odontotermes 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
salmon
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain NGR234; gene azc3656 or dme
Uniprot
Manually annotated by BRENDA team
strain NGR234; gene azc3656 or dme
Uniprot
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
gene Sco2951
-
-
Manually annotated by BRENDA team
gene Sco2951
-
-
Manually annotated by BRENDA team
hexaploid wheat
UniProt
Manually annotated by BRENDA team
hexaploid wheat
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
metabolism
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(2R,3R)-erythrofluoromalate + NAD+
?
show the reaction diagram
-
-
-
-
?
(2S,3R)-tartrate + NAD+
?
show the reaction diagram
-
-
-
-
?
(S)-malate + NAD(P)+
pyruvate + CO2 + NAD(P)H
show the reaction diagram
(S)-malate + NAD+
?
show the reaction diagram
(S)-malate + NAD+
pyruvate + CO2 + NADH
show the reaction diagram
(S)-malate + NAD+
pyruvate + NADH + CO2
show the reaction diagram
-
-
-
-
ir
(S)-malate + NAD+
pyruvate + NADH + H+ + CO2
show the reaction diagram
(S)-malate + NADP+
pyruvate + CO2 + NADPH
show the reaction diagram
(S)-malate + NADP+
pyruvate + NADPH + H+ + CO2
show the reaction diagram
L-aspartate + NAD+
iminopyruvate + CO2 + NADH
show the reaction diagram
-
-
-
-
?
L-malate + NAD+
pyruvate + NADH + H+ + CO2
show the reaction diagram
-
-
-
-
r
malate + NAD+
pyruvate + CO2 + NADH
show the reaction diagram
meso-tartrate + NAD+
?
show the reaction diagram
-
-
-
-
?
pyruvate + CO2 + NADH
(S)-malate + NAD+
show the reaction diagram
pyruvate + NAD+ + HCO3-
(S)-malate + NADH
show the reaction diagram
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
(S)-malate + NAD(P)+
pyruvate + CO2 + NAD(P)H
show the reaction diagram
(S)-malate + NAD+
?
show the reaction diagram
(S)-malate + NAD+
pyruvate + CO2 + NADH
show the reaction diagram
(S)-malate + NAD+
pyruvate + NADH + CO2
show the reaction diagram
-
-
-
-
ir
(S)-malate + NAD+
pyruvate + NADH + H+ + CO2
show the reaction diagram
(S)-malate + NADP+
pyruvate + CO2 + NADPH
show the reaction diagram
(S)-malate + NADP+
pyruvate + NADPH + H+ + CO2
show the reaction diagram
L-malate + NAD+
pyruvate + NADH + H+ + CO2
show the reaction diagram
-
-
-
-
r
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NADPH
-
-
additional information
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ni2+
-
divalent metal ion required, NADP+-linked activity exhibits a maximum at 5 mM Ni2+
Zn2+
5fold activation at 5 mM, only slight activation at 10 mM
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(S)-malate
2-Ketoglutarate
-
-
5'-AMP
-
isozyme NAD-ME2, competitive versus NAD+, mixed inhibition versus (S)-malate
acetyl-CoA
bicarbonate
Bromopyruvate
-
-
Ca2+
inhibits 30% at 1 mM and 60% at 10 mM
citrate
Crassula argentea
-
competitive
Cl-
Crassula argentea
-
-
CO2
-
chimeric mutant NAD-ME1q, mixed inhibition versus NAD+ and (S)-malate; isozyme NAD-ME2 and chimeric mutant NAD-ME1q, mixed inhibition versus NAD+ and (S)-malate
DL-isocitrate
-
-
fructose 6-phosphate
competitive versus (S)-malate, 70% inhibition at 2.5 mM
hydroquinone
-
-
L-asparatate
-
-
L-aspartate
-
slightly competitive to malate, only slight inhibition below pH 6.0
Li+
slight inhibition
Lu3+
-
strong inhibition, reversible slow-binding mechanism, reversible structural interconversion to the Mn2+-binding form, metal binding site structure
malonate
Mn2+
-
inhibits the reductive carboxylation reaction, inhibitory effect is about 20fold reduced by binding of fumarate and L-malate
Na+
complete inhibition at 10 mM, no effect by Na+ at 1 mM
oxalate
oxaloacetate
phosphoenolpyruvate
pyruvate
Tartrate
Tartronate
Urea
-
denaturation, in 3-5 M urea, the enzyme undergoes a reversible tetramer-dimer-monomer quaternary structural change in an acidic pH environment, which resulted in a molten globule state that is prone to aggregate, Mn2+ protects, overview
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1-N6-etheno-CoA
Crassula argentea
-
activates
2-oxoglutarate
-
-
acetyl-CoA
-
;
adenosine 5'-diphosphoglucose
-
activates
ADP
-
slight stimulstion
alpha-D-glucose 1-phosphate
-
activation
AMP
Crassula argentea
-
competitive activation
aspartate
-
stimulates
ATP
-
slight stimulstion
CoA
-
activation kinetics, overview; activation kinetics, overview
coenzyme A
D-fructose 1,6-bisphosphate
-
-
D-fructose 6-phosphate
-
activation
D-glucose 6-phosphate
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activation
fructose 1,6-bisphosphate
fumarate
gamma-amino-n-butyrate
-
slight activation
hydroxy-n-butyrate
-
slight activation
Hydroxypyruvate
-
slight activation
L-malate
NAD+
-
activates the enzyme in mitochondria
oxaloacetate
-
;
phosphoenolpyruvate
SO42-
-
activates
succinate
uridine 5'-diphosphoglucose
-
activates
additional information
-
no activation by CoA and acetyl-CoA, poor activation by ATP and AMP; no activation by oxaloacetate, poor activation by ATP and AMP; poor activation by ATP and AMP
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2
(2R,3R)-erythrofluoromalate
-
25°C
60
(2S)-aspartate
-
25°C
1
(2S)-malate
-
25°C
20
(2S,3R)-tartrate
-
25°C, pH 7.8
0.1 - 57
(S)-malate
13.48 - 16.8
CO2
40
meso-tartrate
-
25°C, pH 7.8
0.018 - 5
NAD+
0.06 - 0.12
NADH
0.207 - 6.12
NADP+
4.1 - 15.03
pyruvate
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
31.1 - 770
(S)-malate
31.1 - 720
NAD+
520
NADP+
pH 7.2, 30°C, with (S)-malate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
10.3 - 3300
(S)-malate
60.2 - 6900
NAD+
2900
NADP+
pH 7.2, 30°C, with (S)-malate
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.45 - 1.5
5'-AMP
3 - 7
CO2
7.4
fructose 6-phosphate
pH 7.2, 30°C, versus (S)-malate
58 - 80
L-aspartate
0.0048 - 0.148
Lu3+
0.041 - 0.15
NADH
0.006
oxalate
-
pH 7.0, 25°C, recombinant wild-type enzyme
0.36
oxaloacetate
pH 7.2, 30°C, versus (S)-malate
11 - 14
pyruvate
0.8 - 4
Tartrate
additional information
additional information
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.017
-
water stress plants at daytime or at nighttime
0.036
-
control plants at daytime
0.107
-
control plants at nighttime
0.201
NAD+-dependent ME activity in the wild-type strain, pH 7.8, 30°C, AZC3656
0.989
-
purified native enzyme, reverse reaction
2.74
-
NAD+-linked activity
4.25
-
purified native enzyme, pH 7.0, 25°C, carboxylation reaction; purified native enzyme, pH 7.0, 25°C, pyruvate carboxylation
5.45
-
NADP+-linked activity
35.4
Crassula argentea
-
-
36
-
purified native enzyme, pH 7.5, 25°C
36.09
-
purified native enzyme, pH 7.5, 25°C, decarboxylation reaction; purified native enzyme, pH 7.5, 25°C, malate decarboxylation
64
purified enzyme, pH 7.2, 30°C
81.5
Crassula argentea
-
-
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6
-
reverse reaction
6.7
-
enzyme complexed to Mg2+ and NAD+
6.9
-
activity with NADP+; with NAD+, without activator
7
-
assay at
7.1
Crassula argentea
-
activated by Mg2+
7.2
-
with NAD+ plus CoA
7.3
-
assay at
7.46
Crassula argentea
-
activated by Mn2+
7.6 - 7.9
-
-
7.8
AZC3656 shows high NAD+-ME activity at pH 7.8, with Michaelis-Menten-like kinetics, at various concentrations of malate, The enzyme exhibits only a very limited positive cooperativity with respect to malate
8.5
-
assay at, oxidation reaction
additional information
-
pH-dependency of the reaction kinetics, overview
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.8 - 7.6
-
pH 5.8: about 60% of maximal activity, pH 7.6: about 40% of maximal activity
6 - 8.5
-
about 40% of maximal activity at pH 6.0 and at pH 8.5
6 - 7.5
-
carboxylation reaction, activity range
6 - 8
-
decarboxylation reaction, activity range
6 - 9
-
activity range, profile overview
7 - 8.7
-
pH 7.0: about 30% of maximal activity, pH 8.7: about 45% of maximal activity
additional information
-
enzyme conformation at different pH values, overview
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30 - 60
-
30°C: about 35% of maximal activity, 60°C: about 50% of maximal activity
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.3
sequence calculation
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
the level of the enzyme in wild-type bacteroids is not limiting for N2-fixation
Manually annotated by BRENDA team
-
; NAD-ME1and -2 subunits show a distinct patterns of accumulation in the separate components of the floral organ; NAD-ME1and -2 subunits show a distinct patterns of accumulation in the separate components of the floral organ
Manually annotated by BRENDA team
-
etiolated
Manually annotated by BRENDA team
-
erythroleukemia cells
Manually annotated by BRENDA team
-
in mesophyll cells, 100% activity is found in cytosol fractions
Manually annotated by BRENDA team
-
NAD-MEH and NADME1 act in concert in this tissue; the NAD-ME1 subunit is present at a slightly higher proportion than the NAD-ME2 subunit, and thus, NAD-MEH and NADME1 act in concert in this tissue; the NAD-ME1 subunit is present at a slightly higher proportion than the NAD-ME2 subunit, and thus, NAD-MEH and NADME1 act in concert in this tissue
Manually annotated by BRENDA team
additional information
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
55000
Crassula argentea
-
x * 55000, alpha, + x * 61000, beta, SDS-PAGE
65000
2 * 65000, alpha-subunit, isozyme NAD-ME1, SDS-PAGE
82000
-
x * 82000, SDS-PAGE
85000
-
4 * 85000, SDS-PAGE
110000
-
mitochondrial isozyme of bundle sheath cells of control and drought-exposed plants
115000
-
cytosolis isozyme of mesophyll and bundle sheath cells of control and drought-exposed plants
117500
gel filtration, isozyme NAD-ME2
119000
Crassula argentea
-
dimer, disc gel electrophoresis
120000
121000
-
mitochondrial isozyme of bundle sheath cells of drought-exposed plants
125000
-
NAD-MEH, gel filtration
170000
-
dimer, gel filtration
200000
-
sucrose density gradient centrifugation
230000
Crassula argentea
-
tetramer, non-denaturing PAGE
231000
Crassula argentea
-
tetramer, disc gel electrophoresis
270000
279000
-
tetramer, gel filtration
300000
-
gel filtration
308000
-
gel filtration
350000
Crassula argentea
-
non-denaturing PAGE
388000
-
gel filtration
400000
-
octamer, gel filtration
490000
491000
Crassula argentea
-
tetramer, disc gel electrophoresis
680000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
decamer
-
10 * 64000, SDS-PAGE
octamer
-
alpha4beta4, 4 * 61000 + 4 * 58000, SDS-PAGE
oligomer
tetramer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
enzyme in binary complex with NAD+, by hanging drop vapour diffusion method, from solution containing 5 mM NAD+, 10 mM tartronate, and 20 mM MgSO4, for cryoprotection soaking overnight in 100 mM Tris-HCl, pH 7.5, with 25% PEG w/v 15 mM NAD+, 10 mM 2-mercaptoethanol, and glycerol up to a final concentration of 20% v/v, X-ray diffraction structure determination and analysis at 2.3 A resolution, structure modeling
-
quarternary complex of purified enzyme with NADH, tartronate, and Mg2+, hanging drop vapour diffusion method, from 100 mM Tris-SO4, pH 7.3, 100 mM sodium acetate, 15% PEG 4000, 5 mM NADH, 10 mM tartronate, 20 mM MgSO4, 10 mM 2-mercaptoethanol, and 0.02% sodium azide, for cryoprotection the crystals are soaked in 25% PEG 4000, 15 mM NAD+, 10 mM 2-mercaptoethanol, and 100 mM Tris-SO4, pH 7.5, for 2 h, then 24 h in the crystallization buffer plus 20% EG v/v, X-ray diffraction structure determination and analysis at 2.0 A resolution, structure modeling
-
enzyme complexed with the natural substrate malate or pyruvate, NAD+ or NADH, Mn2+, and the allosteric activator fumarate, X-ray diffraction structure determination and analysis at 2.1 A resolution, structure modeling
-
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 9
-
25°C, 5 min, stable
286718
8
purified enzyme, most stable at
711524
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
purified enzyme, stable up to, loss of activity above
45
-
15 min, stable at or below
55
-
15 min, complete inactivation
70
purified enzyme, almost complete inactivation
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
freezing of crude enzyme extract treated on Sephadex G-25 destroys activity
-
photooxidation with methylene blue
-
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
photooxidation with methylene blue
-
286701
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, stable for several weeks
-
-80°C, purified native enzyme, 8 months, completely stable
4°C, loss of activity upon prolonged storage
-
crude and partially purified enzyme retains activity for several months when stored as a protein suspension in 75% saturated (NH4)2SO4 solution
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
native enzyme 1500fold to homogeneity by ammonium sulfate fractionation, anion exchange and hydrophobic interaction chromatography, adsorption chromatography, ultrafiltration, and gel filtration
native enzyme 44fold
-
native enzyme 84.7fold by anion exchange and affinity chromatography, and gel filtration; native NAD-preferring malic enzyme 84.7fold by anion exchange and affinity chromatography followed by gel filtration
-
native enzyme from fresh sperm cells by anion exchange and affinity chromatography and gel filtration to over 99% purity
-
native enzyme partially by preparation of mitochondria, method, overview
-
recombinant His-tagged enzyme AZC3656 from Escherichia coli by nickel affinity chromatography
recombinant His-tagged NAD-ME1 and mutants NADME1q and NAD-ME2q from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration; recombinant His-tagged NAD-ME2 and mutants NADME1q and NAD-ME2q from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filteration; recombinant His-tagged NAD-MEH from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
-
recombinant NAD-ME1, NAD-ME2, and NAD-MEH; recombinant NAD-ME1, NAD-ME2, and NAD-MEH
-
several steps
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
DNA and amino acid sequence determination and analysis
DNA and amino acid sequence determination and analysis, expression in Escherichia coli strain JM109
expression of His-tagged NAD-ME1 and of mutants NADME1q and NAD-ME2q in Escherichia coli strain BL21(DE3); expression of His-tagged NAD-ME2 and mutants NADME1q and NAD-ME2q in Escherichia coli strain BL21(DE3); expression of His-tagged NAD-MEH in Escherichia coli strain BL21(DE3)
-
expression of mutant enzymes in Escherichia coli strain M15
-
gene AtNAD-ME1, DNA and amino acid sequence determination and analysis, phylogenetic tree; gene AtNAD-ME2, DNA and amino acid sequence determination and analysis, phylogenetic tree
gene dme or azc3656, DNA and amino acid sequence determination and analysis, expression as His-tagged enzyme in Escherichia coli
gene maeE, is encoded in a cluster consisting of two diverging operons, maePE and maeKR, DNA and amino acid sequence determination and analysis, phylogenetic analysis