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Information on EC 1.1.1.42 - isocitrate dehydrogenase (NADP+) and Organism(s) Arabidopsis thaliana

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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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Arabidopsis thaliana
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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
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
cICDH
CtIDP1
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CtIDP2
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cytosolic NADP-dependent isocitrate dehydrogenase
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IDH
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IDP
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isocitrate dehydrogenase (NADP)
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isocitrate dehydrogenase (NADP-dependent)
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isocitrate dehydrogenase (nicotinamide adenine dinucleotide phosphate)
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NADP isocitric dehydrogenase
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NADP+-linked isocitrate dehydrogenase
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NADP+-specific ICDH
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NADP-dependent isocitrate dehydrogenase
NADP-dependent isocitric dehydrogenase
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NADP-ICDH
NADP-isocitrate dehydrogenase
NADP-linked isocitrate dehydrogenase
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NADP-specific isocitrate dehydrogenase
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oxalosuccinate decarboxylase
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oxalsuccinic decarboxylase
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PS-NADP-IDH
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidative decarboxylation
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redox reaction
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reductive carboxylation
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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
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
D-isocitrate + NADP+
2-oxoglutarate + CO2 + NADPH + H+
show the reaction diagram
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?
isocitrate + NADP+
2-oxoglutarate + CO2 + NADPH + H+
show the reaction diagram
isocitrate + NADP+
2-oxoglutarate + NADPH + H+ + CO2
show the reaction diagram
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-
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?
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
D-isocitrate + NADP+
2-oxoglutarate + CO2 + NADPH + H+
show the reaction diagram
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-
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?
isocitrate + NADP+
2-oxoglutarate + CO2 + NADPH + H+
show the reaction diagram
isocitrate + NADP+
2-oxoglutarate + NADPH + H+ + CO2
show the reaction diagram
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?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NADP+
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
5 mM used in assay conditions
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3-morpholinosydnonimine
44% inhibition at 5 mM of leaf and root enzymes
GSH
inhibits the leaf enzyme by 40% at 5 mM, but not the root enzyme
GSSG
increasing GSSG concentrations progressively inhibit the enzyme activity, almost complete inhibition at 1 mM
H2O2
affects the root enzyme slightly but not the enzyme from leaves
nitrosoglutathione
increasing nitrosoglutathione concentrations progressively inhibit the enzyme activity, complete inhibition at 2 mM
S-nitrosoglutathione
70.5% inhibition at 5 mM of the leaf enzyme, 37.3% of the root enzyme
additional information
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.042 - 0.239
D-isocitrate
0.095 - 0.099
isocitrate
0.0044 - 0.0616
NADP+
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
4.31 - 4.93
isocitrate
5.81
NADP+
wild type enzyme, at pH 7.5 and 25°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
45.4 - 49.7
isocitrate
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5 - 8.5
high activity between pH 7.5 and 8.5
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
Arabidopsis thaliana has three NADP-ICDH genes At1g65930, At5g14590, and At1g54340, coding for the proteins NP_176768, NP_196963, and BT025983, respectively, that are located in different subcellular compartments, i.e. cytosol, chloroplasts, mitochondria, and peroxisomes
physiological function
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cICDH is involved in amino acid synthesis, and plays a role in redox signalling linked to pathogen responses, but cICDH is not required for plant development and primary metabolism in optimal growth conditions
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
ICDHC_ARATH
410
0
45746
Swiss-Prot
other Location (Reliability: 2)
ICDHP_ARATH
485
0
54196
Swiss-Prot
Chloroplast (Reliability: 3)
ICDHX_ARATH
416
0
47234
Swiss-Prot
other Location (Reliability: 1)
A0A1P8ASL1_ARATH
297
0
34126
TrEMBL
other Location (Reliability: 1)
A0A178WDA3_ARATH
297
0
34142
TrEMBL
other Location (Reliability: 1)
A0A178UQB8_ARATH
485
0
54240
TrEMBL
Chloroplast (Reliability: 3)
A0A5S9Y6C3_ARATH
485
0
54196
TrEMBL
Chloroplast (Reliability: 3)
A0A654EU45_ARATH
416
0
47220
TrEMBL
other Location (Reliability: 1)
A0A178W7K0_ARATH
410
0
45746
TrEMBL
other Location (Reliability: 2)
A0A7G2E0U0_ARATH
1637
4
185135
TrEMBL
other Location (Reliability: 1)
A0A7G2E120_ARATH
1630
4
184351
TrEMBL
other Location (Reliability: 1)
A0A7G2FAU1_ARATH
478
0
53267
TrEMBL
Chloroplast (Reliability: 3)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
90000
gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
2 * 48300, His-tagged enzyme, calculated from amino acid sequence
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
glutathionylation
S-glutathionylation of Cys363 is involved in the inhibition of the cytosolic enzyme activity upon nitrosoglutathione treatments
S-nitrosylation
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C363S
the mutation does not perturb the enzymatic characteristics of the enzyme. However, the mutant is less affected by nitrosoglutathione treatment than the wild type enzyme
additional information
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
enzyme activity is affected by oxidative agents like oxidized glutathione and nitrosoglutathione through modifications of conserved Cys residues in the protein
760361
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Ni2+-Sepharose column chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21 cells
gene pICDH, DNA and amino acid sequence determination and analysis, phylogenetic analysis
isozyme cICDH is encoded by a single gene
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Mhamdi, A.; Mauve, C.; Gouia, H.; Saindrenan, P.; Hodges, M.; Noctor, G.
Cytosolic NADP-dependent isocitrate dehydrogenase contributes to redox homeostasis and the regulation of pathogen responses in Arabidopsis leaves
Plant Cell Environ.
33
1112-1123
2010
Arabidopsis thaliana, Arabidopsis thaliana Columbia ecotype
Manually annotated by BRENDA team
Leterrier, M.; Barroso, J.; Palma, J.; Corpas, F.
Cytosolic NADP-isocitrate dehydrogenase in Arabidopsis leaves and roots
Biol. Plant.
56
705-710
2012
Arabidopsis thaliana (Q9SRZ6)
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Manually annotated by BRENDA team
Leterrier, M.; Barroso, J.B.; Valderrama, R.; Begara-Morales, J.C.; Sanchez-Calvo, B.; Chaki, M.; Luque, F.; Vinegla, B.; Palma, J.M.; Corpas, F.J.
Peroxisomal NADP-isocitrate dehydrogenase is required for Arabidopsis stomatal movement
Protoplasma
253
403-415
2016
Arabidopsis thaliana (Q9SLK0), Arabidopsis thaliana Col-0 (Q9SLK0)
Manually annotated by BRENDA team
Niazi, A.; Bariat, L.; Riondet, C.; Carapito, C.; Mhamdi, A.; Noctor, G.; Reichheld, J.
Cytosolic isocitrate dehydrogenase from Arabidopsis thaliana is regulated by glutathionylation
Antioxidants (Basel)
8
16
2019
Arabidopsis thaliana (Q9SRZ6), Arabidopsis thaliana
Manually annotated by BRENDA team