Information on EC 1.1.1.40 - malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)

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

EC NUMBER
COMMENTARY hide
1.1.1.40
-
RECOMMENDED NAME
GeneOntology No.
malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(S)-malate + NADP+ = pyruvate + CO2 + NADPH
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
decarboxylation
-
-
-
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oxidation
-
-
-
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redox reaction
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-
-
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reduction
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-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
C4 and CAM-carbon fixation
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C4 photosynthetic carbon assimilation cycle, NADP-ME type
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C4 photosynthetic carbon assimilation cycle, PEPCK type
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Carbon fixation in photosynthetic organisms
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gluconeogenesis
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gluconeogenesis I
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Metabolic pathways
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Microbial metabolism in diverse environments
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photosynthesis
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Pyruvate metabolism
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SYSTEMATIC NAME
IUBMB Comments
(S)-malate:NADP+ oxidoreductase (oxaloacetate-decarboxylating)
The enzyme catalyses the oxidative decarboxylation of (S)-malate in the presence of NADP+ and divalent metal ions, and the decarboxylation of oxaloacetate. cf. EC 1.1.1.38, malate dehydrogenase (oxaloacetate-decarboxylating), and EC 1.1.1.39, malate dehydrogenase (decarboxylating).
CAS REGISTRY NUMBER
COMMENTARY hide
9028-47-1
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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-
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
Aptenia cordifolia
constitutive CAM plant, 2 isozymes
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-
Manually annotated by BRENDA team
strain NRRL 2270
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-
Manually annotated by BRENDA team
strain NRRL 2270
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Bothriochloa biloba
strain Kuntze
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-
Manually annotated by BRENDA team
Bothriochloa biloba Kuntze
strain Kuntze
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-
Manually annotated by BRENDA team
strain Kuntze
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-
Manually annotated by BRENDA team
strain Kuntze
-
-
Manually annotated by BRENDA team
cultivars Vergasa and Biela
-
-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
Cymbopogon ambiguus
Spreng.
-
-
Manually annotated by BRENDA team
Cymbopogon ambiguus Spreng.
Spreng.
-
-
Manually annotated by BRENDA team
Cymbopogon bombycinus
Spreng.
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-
Manually annotated by BRENDA team
Cymbopogon bombycinus Spreng.
Spreng.
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-
Manually annotated by BRENDA team
Digitaria brownii
-
-
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Manually annotated by BRENDA team
Digitaria smutsi
-
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
gene maeB
UniProt
Manually annotated by BRENDA team
isozyme ChlME1, nuclear encoded, 3'-untranslated region; C3-C4 species, 2 isozymes ChlME1 and ChlME2; isozyme ChlME2, nuclear encoded, 3'-untranslated region; C3-C4 species, 2 isozymes ChlME1 and ChlME2
SwissProt
Manually annotated by BRENDA team
isozyme ChlME1, nuclear encoded, 3'-untranslated region; C4 species, 2 isozymes ChlME1 and ChlME2; isozyme ChlME2, nuclear encoded, 3'-untranslated region; C4 species, 2 isozymes ChlME1 and ChlME2
GenBank
Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
Mnium undulatum
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Manually annotated by BRENDA team
wild-type plants and transgenic plants, expressing potyviral helper component protease HC-pro or Potato virus Y strain NTN
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
Pigeon
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
five NADP-ME genes, PtNADP-ME1, PtNADP-ME2, PtNADP-ME3, PtNADP-ME4, and PtNADPME5
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-
Manually annotated by BRENDA team
salmon
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Manually annotated by BRENDA team
seagull
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Manually annotated by BRENDA team
gene Sco5261
UniProt
Manually annotated by BRENDA team
gene Sco5261
UniProt
Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
strain TV 7-37
SwissProt
Manually annotated by BRENDA team
strain TV 7-37
SwissProt
Manually annotated by BRENDA team
Triticum aestivum Jinmai 47
hexaploid wheat
UniProt
Manually annotated by BRENDA team
; grown in male Wistar rats
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
Trypanosoma brucei stock 427
grown in male Wistar rats
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
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the five PtNADP-ME isoforms cluster in a phylogenetic tree constructed with the whole set of plant NADP-ME sequences, classification into four groups. PtNADP-ME2 and PtNADPME3 cluster with the cytosolic dicot NADP-ME group (group II), while PtNADP-ME4 and PtNADP-ME5 are included in the plastidic dicot NADP-ME group (group III). The group IV comprises both monocot and dicot enzymes, including PtNADP-ME1. Neither of the PtNADP-ME isoforms is included in the monocot NADPMEs (group I)
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
(S)-malate + NAD(P)+
pyruvate + CO2 + NAD(P)H
show the reaction diagram
(S)-malate + NAD+
pyruvate + CO2 + NADH
show the reaction diagram
(S)-malate + NADP+
?
show the reaction diagram
-
-
-
?
(S)-malate + NADP+
pyruvate + CO2 + NADPH
show the reaction diagram
(S)-malate + NADP+
pyruvate + NADPH + CO2
show the reaction diagram
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-
-
-
?
(S)-malate + NADP+
pyruvate + NADPH + H+ + CO2
show the reaction diagram
Oxaloacetate
Pyruvate + CO2
show the reaction diagram
oxaloacetate + NADP+
pyruvate + CO2 + NADPH
show the reaction diagram
-
-
-
-
?
pyruvate + CO2 + NADPH
L-malate + NADP+
show the reaction diagram
pyruvate + NADPH
?
show the reaction diagram
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at 5.4% of the activity of NADP-dependent oxidative decarboxylation of malate
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-
?
additional information
?
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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
P16243
the unique and specialized C4-type enzyme has evolved fro the C3-type enzyme
-
-
?
(S)-malate + NADP+
pyruvate + CO2 + NADPH
show the reaction diagram
(S)-malate + NADP+
pyruvate + NADPH + H+ + CO2
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Cu2+
Pigeon
-
weak activation
KCl
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activates at 2 mM
NH4+
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activates
NH4Cl
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activates
Zn2+
Pigeon
-
weak activation
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(NH4)2SO4
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at high concentrations
(S)-malate
2'-AMP
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competitive
2,3-Butanedione
Pigeon
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pseudo-first-order loss of oxidative decarboxylase activity
2-Ketoglutarate
Aptenia cordifolia
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34% inhibition at 2 mM
2-mercaptoethanol
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inactivation in absence of Mg2+
2-oxoglutarate
5'-AMP
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competitive
acetyl-CoA
adenosine 2'-phosphate
Pigeon
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arsenite
Pigeon
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weak
cAMP
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10% inhibition at 5 mM
citrate
Citric acid
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inhibits all PtNADP-ME activities significantly
CO2
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product inhibition, uncompetitive with respect to L-malate and NADP+, 39% inhibition at 25 mM
Cu2+-ascorbate
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rapid inactivation by generation of reactive oxygen species at pH 5.0, Fe2+ can substitute for Cu2+, Cu2+ or ascorbate alone are not effective, azide, 1,4-diazabicyclo-(2.2.2.)octane, histidine and imidazole protect against inhibition, the substrates L-malate and NADP+ and EDTA protect almost completely, loss of activity is accompanied with cleavage of the protein into 4 fragments of 14-55 kDa
CuCl2
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about 40% loss of activity within 60 min
D-fructose
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PtNADP-ME1
D-fructose-1,6-bisphosphate
D-glucose 6-phosphate
40% inhibition of isozyme NADP-ME1 at 2 mM; inhibition of isozyme NADP-ME2
D-Glucose-6-phosphate
;
Diamide
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2 mM, time-dependent decrease in activity reaching about 40% of initial activity after 60 min. In presence of dithiothreitol, a complete recovery is observed after 90 min. Enzyme oxidation decreases the catalytic activity. No severe loss of protein secondary structure takes place after oxidation; about 40% loss of activity within 60 min
diphenyliodonium chloride
Pigeon
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weak
EDTA
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Fe2+-ascorbate
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rapid inactivation
fumarate
GDP
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13% inhibition at 5 mM
glutathione
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strongly inactivates in absence of Mg2+
H2O2
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83% inhibition at 0.25 mM, 91.1% inhibition at 0.5 mM
Hg2+
Pigeon
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0.0005 mM, almost complete inhibition
iodoacetate
Pigeon
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weak
Iodosobenzoate
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1 mM, time-dependent decrease in activity reaching about 40% of initial activity after 60 min; about 40% loss of activity within 60 min
L-aspartate
Aptenia cordifolia
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competitive, 94% inhibition at 10 mM
L-Malate
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pH 7.0, high concentration
Maleate
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the cis isomer of fumarate, inhibition of isozyme NADP-ME2
malonate
malonyl-CoA
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inhibition of mitochondrial enzyme and cytosolic enzyme to a much lower extent than with acetyl-CoA
NaCl
-
at high concentrations
NAD+
Pigeon
-
weak
NADP+
-
substrate inhibition
NADPH
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product inhibition, competitive with respect to L-malate and NADP+
o-Iodosobenzoate
Pigeon
-
strong
oxalate
oxaloacetate
oxaloacetic acid
p-mercuribenzoate
Pigeon
-
strong
Phenylglyoxal
Pigeon
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pseudo-first-order loss of oxidative decarboxylase activity
phosphate
Aptenia cordifolia
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35% inhibition at 5 mM
phosphoenolpyruvate
pyruvate
sesamol
a specific inhibitor of the enzyme
SO32-
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in decarboxylation of malate: partially competitive with respect to malate, in carboxylation of pyruvate: fully competitive for CO2 or HCO3-
succinate
sulfite
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Tartronate
Trypsin
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digests the mutant enzymes, while the wild-type enzyme is protected in the presence of Mn2+, because a specific cutting site in the Lys352-Gly-Arg354 region is able to generate a unique polypeptide with Mr of 37 kDa, and this polypeptide is resistant to further digestion
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Urea
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inactivation at 3-5 M urea, the pigeon cytosolic NADP+-dependent malic enzyme unfolds and aggregates into various forms with dimers as the basic unit, under the same denaturing conditions but in the presence of 4 mM Mn2+, the enzyme exists exclusively as a molten globule dimer in solution, overview
additional information
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
acetyl carnitine
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19% activation at 5 mM
acetyl-CoA
aspartate
ATP
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18% activation at 5 mM
citrate
D-glucose 6-phosphate
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activates PtNADP-ME3 and PtNADP-ME4
fumarate
L-aspartate
L-glutamate
-
15% activation at 5 mM
malonyl-CoA
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15% activation at 0.005 mM
methanol
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activation is reversible and inversely related to the temperature
palmitoyl-CoA
succinate
UDP
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10% activation at 5 mM
UDP-glucose
Aptenia cordifolia
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32% activation at 2 mM
additional information
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00014 - 36
(S)-malate
13.3 - 27.9
bicarbonate
0.04 - 4.5
L-Malate
1.06 - 3.63
malate
0.25 - 20
NAD+
0.00118 - 116
NADP+
0.002 - 0.06
NADPH
23
NaHCO3
-
-
0.5 - 138.9
pyruvate
additional information
additional information