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Information on EC 1.1.1.37 - malate dehydrogenase and Organism(s) Thermus thermophilus and UniProt Accession P10584
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1.1.1.37 malate dehydrogenaseIUBMB 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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Word Map
- 1.1.1.37
- succinate
- isocitrate
- citrate
- isoenzymes
- oxaloacetate
- isozyme
- glucose-6-phosphate
-
tricarboxylic
- aminotransferase
- phosphoenolpyruvate
- carboxylase
- hexokinase
- dismutase
- esterase
- tca
- alpha-ketoglutarate
- creatine
- fumarase
- aldolase
-
carboxykinase
- transaminase
-
krebs
- phosphoglucomutase
- aconitase
- gpi
-
horn
-
citric
-
medullary
-
phosphofructokinase
- 6-phosphogluconate
-
nadp-dependent
-
trigeminal
-
1.1.1.27
-
allozyme
- meloidogyne
- glyoxysomal
- groes
-
nadp-malate
- alpha-glycerophosphate
- watermelon
-
phosphoglucose
- pqq
-
monomorphic
-
second-stage
-
isoenzymatic
-
root-knot
-
perineal
- diagnostics
- drug development
- biotechnology
- analysis
-
subnucleus
-
quinoproteins
- medicine
- agriculture
-
shsps
The taxonomic range for the selected organisms is: Thermus thermophilus
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
malate dehydrogenase, mdh, mitochondrial malate dehydrogenase, malic dehydrogenase, cytosolic malate dehydrogenase, maldh, nad-dependent malate dehydrogenase, mitochondrial mdh, s-mdh, l-malate dehydrogenase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
(R)-2-hydroxyacid dehydrogenase
-
-
-
-
L-malate dehydrogenase
-
-
-
-
malate (NAD) dehydrogenase
-
-
-
-
malate dehydrogenase (NAD)
-
-
-
-
malic acid dehydrogenase
-
-
-
-
malic dehydrogenase
-
-
-
-
mbNAD-MDH
-
-
-
-
mNAD-MDH
-
-
-
-
NAD-dependent malate dehydrogenase
-
-
-
-
NAD-dependent malic dehydrogenase
-
-
-
-
NAD-L-malate dehydrogenase
-
-
-
-
NAD-linked malate dehydrogenase
-
-
-
-
NAD-malate dehydrogenase
-
-
-
-
NAD-malic dehydrogenase
-
-
-
-
NAD-specific malate dehydrogenase
-
-
-
-
VEG69
-
-
-
-
Vegetative protein 69
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
oxidation
-
-
-
-
reduction
-
-
-
-
PATHWAY SOURCE
PATHWAYS
KEGG
Biosynthesis of secondary metabolites, Carbon fixation in photosynthetic organisms, Carbon fixation pathways in prokaryotes, Citrate cycle (TCA cycle), Cysteine and methionine metabolism, Glyoxylate and dicarboxylate metabolism, Methane metabolism, Microbial metabolism in diverse environments, Pyruvate metabolism
-
-, -, -, -, -, -, -, -, -, -, -, -, -, -, -, -, -, -, -, -, -
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
9001-64-3
-
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
(S)-malate + NAD+
oxaloacetate + NADH + H+
-
-
-
-
r
malate + NAD+
oxaloacetate + NADH + H+
-
-
-
-
r
oxaloacetate + NADH
L-malate + NAD+
-
-
-
-
r
additional information
?
-
crystal structures and molecular dynamics simulations of thermophilic malate dehydrogenase reveal critical loop motion for co-substrate binding
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-
?
additional information
?
-
-
crystal structures and molecular dynamics simulations of thermophilic malate dehydrogenase reveal critical loop motion for co-substrate binding
-
-
?
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
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
NAD+
a slight movement of the enzymes binding loop and few structural elements around the co-substrate binding packet occurs in the presence of NAD+. The overall structures do not change much and retain all related positions
NADPH
mutant EX7 with altered coenzyme specificity from NADH towards NADPH
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
wild-type enzyme and mutant EX7 (with altered coenzyme specificity from NADH towards NADPH)
Uniprot
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
molecular dynamics simulation at higher temperatures were used to reconstruct structures from the crystal structure of TtMDH. At the simulated structure of 80°C, a large change occurs around the active site such that with increasing temperature, a mobile loop is closed to co-substrate binding region. The thermal-induced conformational change of the co-substrate binding loop of TtMDH may contribute to the essential movement of the enzyme for admitting NAD and may benefit the enzyme's activity
additional information
-
molecular dynamics simulation at higher temperatures were used to reconstruct structures from the crystal structure of TtMDH. At the simulated structure of 80°C, a large change occurs around the active site such that with increasing temperature, a mobile loop is closed to co-substrate binding region. The thermal-induced conformational change of the co-substrate binding loop of TtMDH may contribute to the essential movement of the enzyme for admitting NAD and may benefit the enzyme's activity
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). PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
60000
67000
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
additional information
additional information
structure analysis, overview. Similar to other MDHs, a protomer of TtMDH has the N-terminal NAD binding domain and C-terminal catalytic domain and consists of 12 helices and 11 beta-strands. The N-terminal NAD binding domain (residue 1-156) is an open twisted structure with the classical Rossmann fold composed of a parallel six-stranded beta-sheet (beta1-beta6) and four alpha-helices (alpha1-alpha4). The C-terminal catalytic domain comprises an antiparallel twisted five-stranded sheet (beta7-beta11) surrounded by eight alpha-helices
additional information
-
structure analysis, overview. Similar to other MDHs, a protomer of TtMDH has the N-terminal NAD binding domain and C-terminal catalytic domain and consists of 12 helices and 11 beta-strands. The N-terminal NAD binding domain (residue 1-156) is an open twisted structure with the classical Rossmann fold composed of a parallel six-stranded beta-sheet (beta1-beta6) and four alpha-helices (alpha1-alpha4). The C-terminal catalytic domain comprises an antiparallel twisted five-stranded sheet (beta7-beta11) surrounded by eight alpha-helices
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
mutant EX7 (with altered coenzyme specificity from NADH towards NADPH) in complex with NADPH or NADH, 2.0 A resolution
purified recombinant enzyme in apoform and in complex with NAD+, sitting drop vapor diffusion method, mixing 500 nl of 10 mg/ml protein with an equal volume of mother liquor and equilibration against 0.1 ml of the crystallization solution containing 100 mM Tris-HCl, pH 8.2, 22.5% w/v PEG4000, and 200 mM magnesium chloride, at 10°C, 5 days. NAD-bound form crystals are obtained by soaking the apo-form crystal with a 001 ml crystallization reservoir containing 2 mM NAD+ molecule for about 30 min immediately prior X-ray diffraction, X-ray diffraction structure determination and analysis at 1.80-2.36 A resolution, molecular replacement and modelling, overview
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30 - 100
high thermal stability of TtMDH, that does not reach a completely denatured state even at near 100°C
90
90
-
remarkably heat stable without losing activity after incubation for 60 min, 50% activity lost after 30 min at 96°C
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant C-terminally His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene mdh, recombinant expression of C-terminally His-tagged enzyme in Escherichia coli strain BL21(DE3)
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Iijima, S.; Saiki, T.; Beppu, T.
Physicochemical and catalytic properties of thermostable malate dehydrogenase from an extreme thermophile Thermus flavus AT-62
Biochim. Biophys. Acta
613
1-9
1980
Geobacillus stearothermophilus, Bacillus subtilis, Comamonas testosteroni, Escherichia coli, Thermus thermophilus, Sus scrofa, Thermus thermophilus AT-62
Storer, A.C.; Sprott, G.D.; Martin, W.G.
Kinetic and physical properties of the L-malate-NAD+ oxidoreductase from Methanospirillum hungatii and comparison with the enzyme from other sources
Biochem. J.
193
235-244
1981
Bacillus subtilis, Bos taurus, Saccharomyces cerevisiae, Comamonas testosteroni, Escherichia coli, Equus sp., Thermus thermophilus, Gallus sp., Halobacterium salinarum, Methanospirillum hungatei, Mycobacterium sp., Mycolicibacterium phlei, Neurospora crassa, Rattus norvegicus, Salmo sp., Sus scrofa, Thermus aquaticus, Thunnus albacares, Methanospirillum hungatei GPI
Hartl, T.; Grossebueter, W.; Goerisch, H.; Stezowski, J.J.
Crystalline NAD/NADP-dependent malate dehydrogenase; the enzyme from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius
Biol. Chem. Hoppe-Seyler
368
259-267
1987
Escherichia coli, Thermus thermophilus, Methanothermobacter thermautotrophicus, Methanospirillum hungatei, Sulfolobus acidocaldarius, Sus scrofa, Laceyella sacchari, Thermoplasma acidophilum, Thermus aquaticus
Van Kuijk, B.L.M.; Stams, A.J.M.
Purification and characterization of malate dehydrogenase from the syntrophic propionate-oxidizing bacterium strain MPOB
FEMS Microbiol. Lett.
144
141-144
1996
Geobacillus stearothermophilus, Bacillus subtilis, Syntrophobacter fumaroxidans, Chlorobaculum tepidum, Prosthecochloris vibrioformis, Citrullus lanatus, Escherichia coli, Thermus thermophilus, Heliomicrobium gestii, Methanothermus fervidus, Mus musculus, Phenylobacterium immobile, Planomonospora venezuelensis, Streptomyces atratus, Streptosporangium roseum, Syntrophobacter fumaroxidans MPOB
Musrati, R.A.; Kollarova, M.; Mernik, N.; Mikulasova, D.
Malate dehydrogenase: Distribution, function and properties
Gen. Physiol. Biophys.
17
193-210
1998
Saccharomyces cerevisiae, Citrullus lanatus, Escherichia coli, Eucalyptus globulus, Euglena gracilis, Thermus thermophilus, Haloarcula marismortui, Methanothermus fervidus, Mus musculus, Nitzschia alba, Rattus norvegicus, Kitasatospora aureofaciens, Sulfolobus acidocaldarius, Sus scrofa, Zea mays
Kim, S.Y.; Hwang, K.Y.; Kim, S.H.; Sung, H.C.; Han, Y.S.; Cho, Y.
Structural basis for cold adaptation. Sequence, biochemical properties, and crystal structure of malate dehydrogenase from a psychrophile Aquaspirillium arcticum
J. Biol. Chem.
274
11761-11767
1999
Escherichia coli, Thermus thermophilus, Sus scrofa, Aquaspirillum arcticum (Q9ZF99), Aquaspirillum arcticum
Chapman, A.D.M.; Cortes, A.; Dafforn, T.R.; Clarke, A.R.; Brady, R.L.
Structural basis of substrate specificity in malate dehydrogenases: Crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, alpha-ketomalonate and tetrahydoNAD
J. Mol. Biol.
285
703-712
1999
Escherichia coli, Thermus thermophilus, Sus scrofa
Tomita, T.; Fushinobu, S.; Kuzuyama, T.; Nishiyama, M.
Structural basis for the alteration of coenzyme specificity in a malate dehydrogenase mutant
Biochem. Biophys. Res. Commun.
347
502-508
2006
Thermus thermophilus (P10584), Thermus thermophilus
Hung, C.H.; Hwang, T.S.; Chang, Y.Y.; Luo, H.R.; Wu, S.P.; Hsu, C.H.
Crystal structures and molecular dynamics simulations of thermophilic malate dehydrogenase reveal critical loop motion for co-substrate binding
PLoS ONE
8
e83091
2013
Thermus thermophilus (P10584), Thermus thermophilus
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