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Information on EC 1.1.1.42 - isocitrate dehydrogenase (NADP+) and Organism(s) Escherichia coli and UniProt Accession P08200

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EC Tree
IUBMB Comments
Requires Mn2+ or Mg2+ for activity. Unlike EC 1.1.1.41, isocitrate dehydrogenase (NAD+), oxalosuccinate can be used as a substrate. In eukaryotes, isocitrate dehydrogenase exists in two forms: an NAD+-linked enzyme found only in mitochondria and displaying allosteric properties, and a non-allosteric, NADP+-linked enzyme that is found in both mitochondria and cytoplasm . The enzyme from some species can also use NAD+ but much more slowly [6,7].
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Escherichia coli
UNIPROT: P08200
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Word Map
The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
hide(Overall reactions are displayed. Show all >>)
Synonyms
isocitrate dehydrogenase 1, nadp-isocitrate dehydrogenase, nadp-dependent isocitrate dehydrogenase, isocitrate dehydrogenase-1, nadp-icdh, nadp-idh, nadp+-dependent isocitrate dehydrogenase, nadp-linked isocitrate dehydrogenase, nadp-specific isocitrate dehydrogenase, nadp+-specific isocitrate dehydrogenase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
isocitrate dehydrogenase
-
NADP+-isocitrate dehydrogenase
-
CtIDP1
-
-
-
-
CtIDP2
-
-
-
-
IDH
-
-
-
-
IDP
-
-
-
-
isocitrate dehydrogenase (NADP)
-
-
-
-
isocitrate dehydrogenase (NADP-dependent)
-
-
-
-
isocitrate dehydrogenase (nicotinamide adenine dinucleotide phosphate)
-
-
-
-
NADP isocitric dehydrogenase
-
-
-
-
NADP+-dependent isocitrate dehydrogenase
-
-
NADP+-linked isocitrate dehydrogenase
-
-
-
-
NADP+-specific ICDH
-
-
-
-
NADP-dependent isocitrate dehydrogenase
-
-
-
-
NADP-dependent isocitric dehydrogenase
-
-
-
-
NADP-isocitrate dehydrogenase
-
-
NADP-linked isocitrate dehydrogenase
-
-
-
-
NADP-specific isocitrate dehydrogenase
-
-
-
-
oxalosuccinate decarboxylase
-
-
-
-
oxalsuccinic decarboxylase
-
-
-
-
PS-NADP-IDH
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
redox reaction
-
-
-
-
oxidative decarboxylation
-
-
-
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reductive carboxylation
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
isocitrate:NADP+ oxidoreductase (decarboxylating)
Requires Mn2+ or Mg2+ for activity. Unlike EC 1.1.1.41, isocitrate dehydrogenase (NAD+), oxalosuccinate can be used as a substrate. In eukaryotes, isocitrate dehydrogenase exists in two forms: an NAD+-linked enzyme found only in mitochondria and displaying allosteric properties, and a non-allosteric, NADP+-linked enzyme that is found in both mitochondria and cytoplasm [6]. The enzyme from some species can also use NAD+ but much more slowly [6,7].
CAS REGISTRY NUMBER
COMMENTARY hide
9028-48-2
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2-oxoglutarate + NADPH + H+
2-hydroxyglutarate + NADP+
show the reaction diagram
the reaction is catalyzed by mutant enzymes R153H and R153C
-
-
?
isocitrate + NADP+
2-oxoglutarate + CO2 + NADPH + H+
show the reaction diagram
isocitrate + NADP+
2-oxoglutarate + CO2 + NADPH + H+
show the reaction diagram
-
-
-
-
?
isocitrate + NADP+
2-oxoglutarate + NADPH + H+ + CO2
show the reaction diagram
-
-
-
-
?
isopropylmalate + NADP+
?
show the reaction diagram
-
-
-
-
?
additional information
?
-
does not use citrate as substrate
-
-
?
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
isocitrate + NADP+
2-oxoglutarate + CO2 + NADPH + H+
show the reaction diagram
-
-
-
?
isocitrate + NADP+
2-oxoglutarate + NADPH + H+ + CO2
show the reaction diagram
-
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NADP+
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mn2+
2 mM used in assay conditions
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
desferroxamine
-
-
Diethylenetriaminepentaacetic acid
-
-
manganese(III) 5,10,15,20-tetrakis(N-methylpyridinium-2-yl)porphyrin
-
a superoxide dismutase mimic, ICD is inactivated by superoxide, but the inactivated enzyme is replaced by de novo protein synthesis
phosphoenolpyruvate
-
allosteric inhibition. Phosphoenolpyruvate enhances the uncompetitive inhibition of isocitrate lyase by increasing isocitrate, which protects isocitrate dehydrogenase from the inhibition, and contributes to the control through the tricarboxylic acid cycle and glyoxylate shunt
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.2 - 3.3
2-oxoglutarate
0.0217 - 0.0405
isocitrate
0.011 - 0.0392
NADP+
0.00071 - 0.00072
NADPH
0.029
isocitrate
-
-
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1
2-oxoglutarate
0.18 - 106.4
isocitrate
88.1
NADP+
40°C, pH 8.0
additional information
additional information
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.3 - 0.45
2-oxoglutarate
8 - 2600
isocitrate
2200
NADP+
40°C, pH 8.0
additional information
additional information
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.31
phosphoenolpyruvate
-
pH 7.1
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
46200
2 * 46200, estimated from amino acid sequence
85000
Guinier analysis
80000
-
gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 45000, SDS-PAGE
homodimer
2 * 46200, estimated from amino acid sequence
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
R153C
the mutation dramatically reduces the catalytic efficiency of the enzyme for isocitrate oxidation, which drops to 1.5% of the wild type enzyme. The mutant acquires a neomorphic ability of producing 2-hydroxyglutarate from 2-oxoglutarate
R153H
the mutation dramatically reduces the catalytic efficiency of the enzyme for isocitrate oxidation, which drops to 0.6% of the wild type enzyme. The mutant acquires a neomorphic ability of producing 2-hydroxyglutarate from 2-oxoglutarate
C201M
-
higher affinity for NAD+ than for NADP+
C201N
-
higher affinity for NAD+ than for NADP+
C201V
-
higher affinity for NAD+ than for NADP+
S113E
-
affinity for isopropylmalate is 37-fold compared to wild-type
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
t1/2: 24.2 min
additional information
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
His-tagged enzyme is purified by TALON resin column chromatography, ICDH fused maltose-binding protein is purified by amylose resin chromatography
TALON metal affinity resin column chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli Rosetta (DE3) cells
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Ramaley, R.F.; Hudock, M.O.
Purification and properties of isocitrate dehydrogenase (NADP) from Thermus aquaticus YT-1, Bacillus subtilis-168 and Chlamydomonas reinhardti-Y-2
Biochim. Biophys. Acta
315
22-36
1973
Azotobacter vinelandii, Geobacillus stearothermophilus, Bacillus subtilis, Chlamydomonas reinhardtii, Escherichia coli, Thermus aquaticus
Manually annotated by BRENDA team
Seelig, G.F.; Colman, R.F.
Characterization of the physicochemical and catalytic properties of human heart NADP-dependent isocitrate dehydrogenase
Arch. Biochem. Biophys.
188
394-409
1978
Escherichia coli, Homo sapiens
Manually annotated by BRENDA team
Vasquez, B.; Reeves, H.C.
NADP-specific isocitrate dehydrogenase from Escherichia coli. V. Multiple forms of the enzyme
Biochim. Biophys. Acta
660
16-22
1981
Escherichia coli
Manually annotated by BRENDA team
Doyle, S.A.; Beernink, B.T.; Koshland, Jr., D.E.
Structural basis for a change in substrate specificity: crystal structur of S113E isocitrate dehydrogenase in a complex with isopropylmalate, Mg2+, and NAPD
Biochemistry
40
4234-4241
2001
Escherichia coli
Manually annotated by BRENDA team
Chen, R.; Greer, A.F.; Dean, A.M.
Structural constrains in protein engineering. The coenzyme specificity of Escherichia coli isocitrate dehydrogenase
Eur. J. Biochem.
250
578-582
1997
Escherichia coli
Manually annotated by BRENDA team
Ogawa, T.; Murakami, K.; Mori, H.; Ishii, N.; Tomita, M.; Yoshin, M.
Role of phosphoenolpyruvate in the NADP-isocitrate dehydrogenase and isocitrate lyase reaction in Escherichia coli
J. Bacteriol.
189
1176-1178
2007
Escherichia coli
Manually annotated by BRENDA team
Tsuchiya, D.; Shimizu, N.; Tomita, M.
Versatile architecture of a bacterial aconitase B and its catalytic performance in the sequential reaction coupled with isocitrate dehydrogenase
Biochim. Biophys. Acta
1784
1847-1856
2008
Escherichia coli (P08200)
Manually annotated by BRENDA team
Batinic-Haberle, I.; Benov, L.T.
An SOD mimic protects NADP+-dependent isocitrate dehydrogenase against oxidative inactivation
Free Radic. Res.
42
618-624
2008
Escherichia coli, Rattus norvegicus
Manually annotated by BRENDA team
Stokke, R.; Karlstroem, M.; Yang, N.; Leiros, I.; Ladenstein, R.; Birkeland, N.K.; Steen, I.H.
Thermal stability of isocitrate dehydrogenase from Archaeoglobus fulgidus studied by crystal structure analysis and engineering of chimers
Extremophiles
11
481-493
2007
Archaeoglobus fulgidus (O29610), Archaeoglobus fulgidus, Escherichia coli (P08200), Escherichia coli
Manually annotated by BRENDA team
Song, P.; Li, S.; Wu, Y.; Lv, C.; Wang, P.; Zhu, G.
Point mutation (R153H or R153C) in Escherichia coli isocitrate dehydrogenase Biochemical characterization and functional implication
J. Basic Microbiol.
57
41-49
2017
Escherichia coli (P08200), Escherichia coli
Manually annotated by BRENDA team