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Information on EC 1.1.1.37 - malate dehydrogenase and Organism(s) Arabidopsis thaliana and UniProt Accession Q9ZP06

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EC Tree
     1 Oxidoreductases
         1.1 Acting on the CH-OH group of donors
             1.1.1 With NAD+ or NADP+ as acceptor
                1.1.1.37 malate dehydrogenase
IUBMB Comments
There are several forms of malate dehydrogenases that differ by their use of substrate and cofactors. This NAD+-dependent enzyme forms oxaloacetate and unlike EC 1.1.1.38, malate dehydrogenase (oxaloacetate-decarboxylating), is unable to convert it to pyruvate. Also oxidizes some other 2-hydroxydicarboxylic acids. cf. EC 1.1.1.82, malate dehydrogenase (NADP+); EC 1.1.1.299, malate dehydrogenase [NAD(P)+]; and EC 1.1.5.4, malate dehydrogenase (quinone).
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This record set is specific for:
Arabidopsis thaliana
UNIPROT: Q9ZP06
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Word Map
The taxonomic range for the selected organisms is: Arabidopsis thaliana
The enzyme appears in selected viruses and cellular organisms
Synonyms
malate dehydrogenase, mdh, mitochondrial malate dehydrogenase, malic dehydrogenase, cytosolic malate dehydrogenase, nad-dependent malate dehydrogenase, maldh, mitochondrial mdh, s-mdh, l-malate dehydrogenase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
mitochondrial malate dehydrogenase
-
mitochondrial MDH
-
NAD-dependent MDH
-
(R)-2-hydroxyacid dehydrogenase
-
-
-
-
cyMDH1
-
isoform
cyMDH2
-
isoform
cyMDH3
-
isoform
cytosolic malate dehydrogenase
-
L-malate dehydrogenase
-
-
-
-
L-malate-NAD-oxidoreductase
-
-
L-malate:NAD oxidoreductase
-
malate (NAD) dehydrogenase
-
-
-
-
malate dehydrogenase (NAD)
-
-
-
-
malic acid dehydrogenase
-
-
-
-
malic dehydrogenase
-
-
-
-
mbNAD-MDH
-
-
-
-
mitochondrial malate dehydrogenase
-
mitochondrial MDH
-
mNAD-MDH
-
-
-
-
NAD+ malate dehydrogenase
-
-
NAD+-MDH enzymes
-
-
NAD-dependent malate dehydrogenase
NAD-dependent malic dehydrogenase
-
-
-
-
NAD-dependent MDH
NAD-L-malate dehydrogenase
-
-
-
-
NAD-linked malate dehydrogenase
-
-
-
-
NAD-malate dehydrogenase
NAD-malic dehydrogenase
-
-
-
-
NAD-MDH
NAD-specific malate dehydrogenase
-
-
-
-
pdNAD-MDH
peroxisomal NAD+-malate dehydrogenase 1
-
-
peroxisomal NAD+-malate dehydrogenase 2
-
-
plastid-localized NAD-dependent MDH
-
plastidial NAD+-dependent malate dehydrogenase
-
-
plastidial NAD-dependent malate dehydrogenase
VEG69
-
-
-
-
Vegetative protein 69
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
-
-
-
-
reduction
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
(S)-malate:NAD+ oxidoreductase
There are several forms of malate dehydrogenases that differ by their use of substrate and cofactors. This NAD+-dependent enzyme forms oxaloacetate and unlike EC 1.1.1.38, malate dehydrogenase (oxaloacetate-decarboxylating), is unable to convert it to pyruvate. Also oxidizes some other 2-hydroxydicarboxylic acids. cf. EC 1.1.1.82, malate dehydrogenase (NADP+); EC 1.1.1.299, malate dehydrogenase [NAD(P)+]; and EC 1.1.5.4, malate dehydrogenase (quinone).
CAS REGISTRY NUMBER
COMMENTARY hide
9001-64-3
-
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+
oxaloacetate + NADH + H+
show the reaction diagram
-
-
-
r
(S)-malate + NAD+
oxaloacetate + NADH + H+
show the reaction diagram
malate + NAD+
oxaloacetate + NADH + H+
show the reaction diagram
-
-
-
-
r
oxaloacetate + NADH
L-malate + NAD+
show the reaction diagram
-
-
-
-
r
oxaloacetate + NADH + H+
(S)-malate + NAD+
show the reaction diagram
additional information
?
-
-
PMDH activity is not essential for photosynthesis in air in Arabidopsis
-
-
?
NATURAL SUBSTRATE
NATURAL 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+
oxaloacetate + NADH + H+
show the reaction diagram
-
-
-
r
(S)-malate + NAD+
oxaloacetate + NADH + H+
show the reaction diagram
malate + NAD+
oxaloacetate + NADH + H+
show the reaction diagram
-
-
-
-
r
oxaloacetate + NADH + H+
(S)-malate + NAD+
show the reaction diagram
additional information
?
-
-
PMDH activity is not essential for photosynthesis in air in Arabidopsis
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
-
0.1 mM used in assay conditions
Mn2+
24% activation at 5 mM
additional information
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2,4-dichlorophenoxybutyric acid
-
-
Cu2+
complete inhibition at 5 mM
Diamide
-
isoforms cy MDH1 and cyMDH2 are reversibly inactivated by diamide treatment. Both NADH and GSH separately or together prevented inactivation of cyMDH1 and cyMDH2 by diamide
Fe3+
complete inhibition at 5 mM
Zn2+
42% inhibition at 5 mM
additional information
-
isoform cyMDH3 maintains its low basal activity upon oxidation with 0.5 mM diamide
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.05 - 0.431
NADH
0.143 - 0.324
oxaloacetate
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
343 - 677
NADH
351 - 608
oxaloacetate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
6900 - 9000
NADH
2500 - 2600
oxaloacetate
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 10
maximal activity at pH 7.5, 70% of maximal activity at pH 10.0, 40% at pH 7.0, 20% at pH 5.0, very low activity below pH 5.0 and above pH 10.0
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
mMDH1; isozymes mMDH1 and mMDH2, eight genes encoding isoforms of NAD-dependent MDH
UniProt
Manually annotated by BRENDA team
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
from long-daygrown plants
Manually annotated by BRENDA team
additional information
isozyme pdNAD-MDH is expressed in green and nongreen tissues throughout development and the diurnal cycle
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
highly expressed mMDH1 and lower expressed mMDH2 isoforms
Manually annotated by BRENDA team
-
nuclear localization of cyMDH isoforms is significantly increased under oxidizing conditions in isolated Arabidopsis protoplasts, in particular of isoform cyMDH3
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
mMDH has a role in maximizing the photorespiratory rate. The slow-growing mmdh1mmdh2 mutant has elevated leaf respiration rate in the dark and light, without loss of photosynthetic capacity, suggesting that mMDH normally uses NADH to reduce oxaloacetate to malate, which is then exported to the cytosol, rather than to drive mitochondrial respiration. Increased respiratory rate in leaves can account in part for the low net CO2 assimilation and slow growth rate of mmdh1mmdh2. Loss of mMDH also affects photorespiration with alterations in CO2 assimilation/intercellular CO2 at low CO2, and the light-dependent elevated concentration of photorespiratory metabolites
evolution
Arabidopsis thaliana contains 10 MDHs with only one single copy of MDH gene in the chloroplast, which is a plastidlocalized NAD-dependent MDH
malfunction
metabolism
the enzyme is more efficient in the reductive reaction in the tricarboxylic acid cycle
physiological function
additional information
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
MDHM1_ARATH
341
0
35804
Swiss-Prot
Mitochondrion (Reliability: 4)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
67000
about, recombinant detagged mature enzyme, gel filtration
70000
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
-
x * 35000, SDS-PAGE
homodimer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method, using 0.18 M ammonium sulfate, 0.09 M sodium acetate trihydrate, pH 4.6, 27% (w/v) polyethylene glycol monomethyl ether 2000, and 10% (v/v) glycerol
purified recombinant detagged enzyme, hanging drop vapor diffusion method, mixing of 0.0003 ml 6 mg/ml protein in 20 mM Tris-HCl, pH 8.0, 200 mM NaCl, and 10% glycerol, with 0.0003 ml of reservoir solution containing 1.2 M sodium citrate tribasic dihydrate, pH 7.0, 20°C, method optimization, X-ray diffraction structure determination and analysis
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C125S
-
the mutant of isoform cyMDH1 shows slightly increased activity compared to the wild type enzyme. The mutant of isoform cyMDH2 shows slightly decreased activity compared to the wild type enzyme
C131S
-
the mutant of isoform cyMDH3 shows decreased activity compared to the wild type enzyme
C155S
-
the mutant of isoform cyMDH1 shows slightly increased activity compared to the wild type enzyme. The mutant of isoform cyMDH2 shows slightly decreased activity compared to the wild type enzyme
C161S
-
the mutant of isoform cyMDH3 shows decreased activity compared to the wild type enzyme
C252S
-
the mutant of isoform cyMDH1 shows strongly decreased activity compared to the wild type enzyme. The mutant of isoform cyMDH2 shows slightly decreased activity compared to the wild type enzyme
C258S
-
the mutant of isoform cyMDH3 shows decreased activity compared to the wild type enzyme
C279S
-
the mutant of isoform cyMDH3 shows wild type activity
C292S
-
the mutant of isoform cyMDH1 shows slightly increased activity compared to the wild type enzyme. The mutant of isoform cyMDH2 shows slightly decreased activity compared to the wild type enzyme
C298S
-
the mutant of isoform cyMDH3 shows wild type activity
C2S
-
the mutant of isoform cyMDH3 shows strongly increased activity compared to the wild type enzyme
C330S
-
the mutant of isoform cyMDH1 shows slightly decreased activity compared to the wild type enzyme and is not inhibited by diamide. The mutant of isoform cyMDH2 shows decreased activity compared to the wild type enzyme and is not inhibited by diamide
C336S
-
the mutant of isoform cyMDH3 shows wild type activity
C79S
-
the mutant of isoform cyMDH1 shows slightly increased activity compared to the wild type enzyme. The mutant of isoform cyMDH2 shows slightly decreased activity compared to the wild type enzyme
C85S
-
the mutant of isoform cyMDH3 shows slightly decreased activity compared to the wild type enzyme
R162Q
-
inactive
R162Q/R234Q
-
inactive
R234Q
-
inactive
additional information
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
49.9 - 54.7
the melting temperature of the reduced isoform cytMDH1 is 54.7°C, while the melting temperature of the oxidized isoform cytMDH1 drops by to 49.9°C
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
the enzyme is sensitive to H2O2 stress. The impact of H2O2 on enzyme activities is probably due to posttranslational modifications
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Ni-Sepharose 6 column chromatography
-
Ni2+-Sepharose column chromatography
recombinant His-Sumo-tagged enzyme from Escherichia coli stain BL21 (DE3) by nickel affinity chromatography, proteolytic cleavage of the His-Sumo tag, ultrafiltration, and gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene mmdh1, genotyping
expressed in Escherichia coli BL21 (DE3) pLysS cells
-
expressed in Escherichia coli BL21(DE3) CodonPlus cells and in Nicotiana benthamiana leaves
-
expressed in Escherichia coli C41(DE3) cells
gene mdh, sequence comparisons, recombinant expression of N-terminally His-Sumo-tagged enzyme in Escherichia coli stain BL21 (DE3)
gene mmdh2, genotyping
genes pmdh1 and pmdh2
-
quantitative reverse transcription PCR enzyme expression analyssis
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Potvin, C.; Simon, J.P.; Blanchard, M.H.
Thermal properties of NAD malate dehydrogenase and glutamate oxaloacetate transaminase in two genotypes of Arabidopsis thaliana (Cruciferae) from contrasting environments
Plant Sci. Lett.
31
35-47
1983
Arabidopsis thaliana, Lathyrus japonicus, Phaseolus acutifolius, Phaseolus vulgaris, Spirodela polyrhiza, Viola sp.
-
Manually annotated by BRENDA team
Cuevas, I.C.; Podesta, F.E.
Purification and physical and kinetic characterization of an NAD+-dependent malate dehydrogenase from leaves of pineapple (Ananas comosus)
Physiol. Plant.
108
240-248
2000
Ananas comosus, Arabidopsis thaliana, Bryophyllum calycinum, Citrullus lanatus, Echinococcus granulosus, Mesembryanthemum crystallinum, Opuntia ficus-indica, Zea mays
-
Manually annotated by BRENDA team
Pracharoenwattana, I.; Cornah, J.E.; Smith, S.M.
Arabidopsis peroxisomal malate dehydrogenase functions in beta-oxidation but not in the glyoxylate cycle
Plant J.
50
381-390
2007
Arabidopsis thaliana
Manually annotated by BRENDA team
Cousins, A.B.; Pracharoenwattana, I.; Zhou, W.; Smith, S.M.; Badger, M.R.
Peroxisomal malate dehydrogenase is not essential for photorespiration in Arabidopsis but its absence causes an increase in the stoichiometry of photorespiratory CO2 release
Plant Physiol.
148
786-795
2008
Arabidopsis thaliana
Manually annotated by BRENDA team
Tomaz, T.; Bagard, M.; Pracharoenwattana, I.; Linden, P.; Lee, C.P.; Carroll, A.J.; Stroeher, E.; Smith, S.M.; Gardestroem, P.; Millar, A.H.
Mitochondrial malate dehydrogenase lowers leaf respiration and alters photorespiration and plant growth in Arabidopsis
Plant Physiol.
154
1143-1157
2010
Arabidopsis thaliana (Q9LKA3), Arabidopsis thaliana (Q9ZP06)
Manually annotated by BRENDA team
An, Y.; Cao, Y.; Xu, Y.
Purification and characterization of the plastid-localized NAD-dependent malate dehydrogenase from Arabidopsis thaliana
Biotechnol. Appl. Biochem.
63
490-496
2016
Arabidopsis thaliana (Q9SN86), Arabidopsis thaliana
Manually annotated by BRENDA team
Beeler, S.; Liu, H.C.; Stadler, M.; Schreier, T.; Eicke, S.; Lue, W.L.; Truernit, E.; Zeeman, S.C.; Chen, J.; Koetting, O.
Plastidial NAD-dependent malate dehydrogenase is critical for embryo development and heterotrophic metabolism in Arabidopsis
Plant Physiol.
164
1175-1190
2014
Arabidopsis thaliana (Q9SN86)
Manually annotated by BRENDA team
Liszka, A.; Schimpf, R.; Cartuche Zaruma, K.I.; Buhr, A.; Seidel, T.; Walter, S.; Knuesting, J.; Dreyer, A.; Dietz, K.J.; Scheibe, R.; Selinski, J.
Three cytosolic NAD-malate dehydrogenase isoforms of Arabidopsis thaliana on the crossroad between energy fluxes and redox signaling
Biochem. J.
477
3673-3693
2020
Arabidopsis thaliana
Manually annotated by BRENDA team
Huang, J.; Niazi, A.K.; Young, D.; Rosado, L.A.; Vertommen, D.; Bodra, N.; Abdelgawwad, M.R.; Vignols, F.; Wei, B.; Wahni, K.; Bashandy, T.; Bariat, L.; Van Breusegem, F.; Messens, J.; Reichheld, J.P.
Self-protection of cytosolic malate dehydrogenase against oxidative stress in Arabidopsis
J. Exp. Bot.
69
3491-3505
2018
Arabidopsis thaliana (P93819)
Manually annotated by BRENDA team
Smith, S.
Moonlighting NAD+ malate dehydrogenase is essential for chloroplast biogenesis
Plant Cell
30
1663-1664
2018
Arabidopsis thaliana
Manually annotated by BRENDA team
Demarsy, E.; Albertini, D.; Maier, B.A.; Kessler, F.; Hoertensteiner, S.; Zeeman, S.C.; Koetting, O.
Plastidial NAD-dependent malate dehydrogenase A moonlighting protein involved in early chloroplast development through its interaction with an FtsH12-FtsHi protease complex
Plant Cell
30
1745-1769
2018
Arabidopsis thaliana
Manually annotated by BRENDA team