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Information on EC 1.1.1.42 - isocitrate dehydrogenase (NADP+) and Organism(s) Mycobacterium tuberculosis and UniProt Accession O53611
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1.1.1.42 isocitrate dehydrogenase (NADP+)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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- 1.1.1.42
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malic
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idh1-mutant
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tricarboxylic
-
hypermethylation
- multiforme
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high-grade
-
progression-free
- temozolomide
- 2-oxoglutarate
-
radiotherapy
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codeletion
-
neomorphic
- alpha-ketoglutarate
- 6-phosphogluconate
-
nadph-generating
- cholangiocarcinomas
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o6-methylguanine-dna
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gliomagenesis
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proneural
The taxonomic range for the selected organisms is: Mycobacterium tuberculosis
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
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
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
CtIDP1
-
-
-
-
CtIDP2
-
-
-
-
IDH
-
-
-
-
IDP
-
-
-
-
isocitrate dehydrogenase (NADP)
-
-
-
-
isocitrate dehydrogenase (NADP-dependent)
-
-
-
-
isocitrate dehydrogenase (nicotinamide adenine dinucleotide phosphate)
-
-
-
-
NADP isocitric dehydrogenase
-
-
-
-
NADP+-linked isocitrate dehydrogenase
-
-
-
-
NADP+-specific ICDH
-
-
-
-
NADP-dependent isocitrate dehydrogenase
-
-
-
-
NADP-dependent isocitric dehydrogenase
-
-
-
-
NADP-linked isocitrate dehydrogenase
-
-
-
-
NADP-specific isocitrate dehydrogenase
oxalosuccinate decarboxylase
-
-
-
-
oxalsuccinic decarboxylase
-
-
-
-
PS-NADP-IDH
-
-
-
-
NADP-specific isocitrate dehydrogenase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH + H+
protonation of the enolate to form product 2-oxoglutarate is the rate-limiting step
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
redox reaction
-
-
-
-
oxidative decarboxylation
-
-
-
-
reductive carboxylation
-
-
-
-
PATHWAY SOURCE
PATHWAYS
KEGG
-
-, -, -, -, -, -, -, -, -, -, -, -
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
9028-48-2
-
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
isocitrate + NADP+
2-oxoglutarate + CO2 + NADPH + H+
-
-
-
?
isocitrate + NADP+
2-oxoglutarate + CO2 + NADPH + H+
-
-
-
?
isocitrate + NADP+
2-oxoglutarate + CO2 + NADPH + H+
-
-
-
?
additional information
?
-
Mycobacterium tuberculosis ICDH-1 also catalyzes the formation of 2-hydroxyglutarate
-
-
?
additional information
?
-
-
Mycobacterium tuberculosis ICDH-1 also catalyzes the formation of 2-hydroxyglutarate
-
-
?
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
isocitrate + NADP+
2-oxoglutarate + CO2 + NADPH + H+
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
no acitivty of isoforms with Mn2+ or Ca2+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
NaCl
-
isoform ICD-2, increase in activity in up to 200 mM NaCl. Isoform ICD-1, no influence of NaCl. Above 200 mM, NaCl is inhibitory
NADPH
product inhibition competitive versus NADP+ and noncompetitive versus isocitrate
additional information
product inhibition patterns for ICDH-1, overview
-
additional information
-
product inhibition patterns for ICDH-1, overview
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
NaCl
-
isoform ICD-2, increase in activity in up to 200 mM NaCl. Isoform ICD-1, no influence of NaCl. Above 200 mM, NaCl is inhibitory
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.05
isocitrate
pH 7.5, temperature not specified in the publication, recombinant His-tagged enzyme
0.01
DL-isocitrate
-
isoform ICD-1, presence of Mg2+, pH 7.5, 25°C
0.02
DL-isocitrate
-
isoform ICD-2, presence of Mg2+, pH 7.5, 25°C
0.022
DL-isocitrate
-
isoform ICD-1, presence of Zn2+, pH 7.5, 25°C
0.015
NADP+
pH 7.5, temperature not specified in the publication, recombinant His-tagged enzyme
additional information
additional information
steady-state kinetics, kinetic mechanism of ICDH-1, overview
-
additional information
additional information
-
steady-state kinetics, kinetic mechanism of ICDH-1, overview
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
33
isocitrate
pH 7.5, temperature not specified in the publication, recombinant His-tagged enzyme
19.6
DL-isocitrate
-
isoform ICD-2, presence of Mg2+, pH 7.5, 25°C
33
NADP+
pH 7.5, temperature not specified in the publication, recombinant His-tagged enzyme
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5.5
-
isoform ICD-1, 30% of maximum activity, isoform ICD-2, 10% of maximum activity
9.5
-
isoform ICD-1, 90% of maximum activity, isoform ICD-2, less than 40% of maximum activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
60
-
isoform ICD-1, 40% residual activity, ICD-2, 5% residual activity
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
49000
86000
49000
-
2 * 49000, isoform ICD-1, 2 * 86000, isoform ICD-2, SDS-PAGE. Besides dimers, isoform ICD-1 forms some tetramer, ICD-2 forms trimer
49000
-
4 * 49000, isoform ICD-1, SDS-PAGE. Main form is dimer for isoform ICD-1
86000
-
2 * 49000, isoform ICD-1, 2 * 86000, isoform ICD-2, SDS-PAGE. Besides dimers, isoform ICD-1 forms some tetramer, ICD-2 forms trimer
86000
-
and dimer, 3 * 86000, SDS-PAGE and chemical crosslinking, isoform ICD-2
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
homodimer
each subunit has a Rossmann fold, and a common top domain of interlocking beta sheets
tetramer
-
4 * 49000, isoform ICD-1, SDS-PAGE. Main form is dimer for isoform ICD-1
trimer
-
and dimer, 3 * 86000, SDS-PAGE and chemical crosslinking, isoform ICD-2
additional information
dimer
-
2 * 49000, isoform ICD-1, 2 * 86000, isoform ICD-2, SDS-PAGE. Besides dimers, isoform ICD-1 forms some tetramer, ICD-2 forms trimer
additional information
three-dimensional structure of Mtb ICDH-1, overview
additional information
-
three-dimensional structure of Mtb ICDH-1, overview
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified ICDH-1 in complex with NADPH at Mn2+, hanging drop vapor diffusion method, 0.001 ml of protein in 5 mM NADPH, and 5 mM MnCl2 is mixed with 0.001 ml of reservoir solution containing 30% PEG 2000 and 0.1 M Tris-HCl, pH 8.0, room temperature, X-ray diffraction structure determination and analysis at 2.18 A resoltuion
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
65
-
30 min, isoform ICD-1, irreversible thermal inactivation, isoform ICD-2, renaturation of inactivated protein by slow cooling till 55°C
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant N-terminally His6-tagged enzyme by nickel affinity chromatography and gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene Rv3339c, expression of N-terminally His6-tagged enzyme
RENATURED/Commentary
ORGANISM
UNIPROT
LITERATURE
isoform ICD-2, renaturation of protein inactivated for 30 min at 65°C by slow cooling till 55°C
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Plaut, G.W.E.
Isocitrate dehydrogenase
The Enzymes, 2nd Ed. (Boyer, P. D. , Lardy, H. , Myrbck, K. , eds. )
7
105-126
1963
Aspergillus niger, Saccharomyces cerevisiae, Citrobacter freundii, Mycobacterium tuberculosis, Sus scrofa, Trypanosoma cruzi
-
Banerjee, S.; Nandyala, A.; Podili, R.; Katoch, V.M.; Hasnain, S.E.
Comparison of Mycobacterium tuberculosis isocitrate dehydrogenases (ICD-1 and ICD-2) reveals differences in coenzyme affinity, oligomeric state, pH tolerance and phylogenetic affiliation
BMC Biochem.
6
20
2005
Mycobacterium tuberculosis
Vinekar, R.; Ghosh, I.
Determination of phosphorylation sites for NADP-specific isocitrate dehydrogenase from Mycobacterium tuberculosis
J. Biomol. Struct. Dyn.
26
741-754
2009
Mycobacterium tuberculosis (A5U813), Mycobacterium tuberculosis (O53611), Mycobacterium tuberculosis
Quartararo, C.E.; Hazra, S.; Hadi, T.; Blanchard, J.S.
Structural, kinetic and chemical mechanism of isocitrate dehydrogenase-1 from Mycobacterium tuberculosis
Biochemistry
52
1765-1775
2013
Mycobacterium tuberculosis (P9WKL1), Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv (P9WKL1)
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