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Literature summary extracted from

  • Xu, X.; Zhao, J.; Xu, Z.; Peng, B.; Huang, Q.; Arnold, E.; Ding, J.
    Structures of human cytosolic NADP-dependent isocitrate dehydrogenase reveal a novel self-regulatory mechanism of activity (2004), J. Biol. Chem., 279, 33946-33957.
    View publication on PubMed

Activating Compound

EC Number Activating Compound Comment Organism Structure
1.1.1.42 additional information glucose induces epression of isozyme IDP1, glycerol induces epression of isozymes IDP1 and IDP2, fatty acids induce epression of isozymes IDP1, IDP2, and IDP3 Saccharomyces cerevisiae

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.1.1.42 expression of C-terminally His-tagged enzyme in Escherichia coli BL21(DE3) Homo sapiens
1.1.1.42 expression of isozyme IDP1 and IDP2 as His-tagged enzymes in a disruption mutant Saccharomyces cerevisiae

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.1.1.42 hanging drop vapour diffusion method, purified recombinant His-tagged enzyme in complex with NADP+: equal volume of protein solution, containing 15 mg/ml enzyme, 20 mM Tris-HCl, pH 7.4, 100 mM NaCl, and 10 mM NADP+, and of reservoir solution, containing 100 mM MES, pH 6.5, 12% PEG 20000, at 4°C, purified recombinant His-tagged enzyme in complex with NADP+, isocitrate and Ca2+: equal volume of protein solution, containing 15 mg/ml enzyme, 20 mM Tris-HCl, pH 7.4, 100 mM NaCl, and 10 mM NADP+, 10 mM DL-isocitrate and 10 mM CaCl2, and of reservoir solution, containing 100 mM MES, pH 5.9, 20% PEG 6000, at 20°C, X-ray diffraction structure determination and analysis Homo sapiens

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
1.1.1.42 additional information
-
 additional information kinetics of isozymes IDP1 and IDP2 Saccharomyces cerevisiae

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
1.1.1.42 cytosol
-
 Homo sapiens 5829
-
1.1.1.42 cytosol isozyme IDP2 Saccharomyces cerevisiae 5829
-
1.1.1.42 mitochondrion isozyme IDP1 Saccharomyces cerevisiae 5739
-
1.1.1.42 peroxisome isoyzme IDP3 Saccharomyces cerevisiae 5777
-

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
1.1.1.42 Ca2+ divalent metal ion is required, binding structure and conformation at the isocitrate-metal-binding site Homo sapiens
1.1.1.42 Mg2+
-
 Saccharomyces cerevisiae
1.1.1.42 Mg2+ divalent metal ion is required, binding structure and conformation at the isocitrate-metal-binding site Homo sapiens

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
1.1.1.42 46381
-
 x * 46381, isozyme IDP1, mass spectrometry, x * 46562, isozyme IDP2, mass spectrometry, x * 47856, isozyme IDP3, mass spectrometry Saccharomyces cerevisiae
1.1.1.42 46562
-
 x * 46381, isozyme IDP1, mass spectrometry, x * 46562, isozyme IDP2, mass spectrometry, x * 47856, isozyme IDP3, mass spectrometry Saccharomyces cerevisiae
1.1.1.42 47856
-
 x * 46381, isozyme IDP1, mass spectrometry, x * 46562, isozyme IDP2, mass spectrometry, x * 47856, isozyme IDP3, mass spectrometry Saccharomyces cerevisiae

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.1.1.42 D-isocitrate + NADP+ Saccharomyces cerevisiae the reaction is reversible for isozyme IDP2 2-oxoglutarate + CO2 + NADPH
-
 r
1.1.1.42 isocitrate + NADP+ Homo sapiens enzyme has a self-regulatory mechanism of activity mimicking the phosphorylation mechanism of bacterial enzymes 2-oxoglutarate + CO2 + NADPH + H+
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
1.1.1.42 Homo sapiens
-
-
-
1.1.1.42 Saccharomyces cerevisiae
-
 1 cytosolic, 1 peroxisomal, and 1 mitochondrial isozyme
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.1.1.42 recombinant His-tagged enzyme from Escherichia coli by nickel affinity chromatography Homo sapiens
1.1.1.42 recombinant His-tagged isozymes IDP1 and IDP2 by nickel affinity chromatography Saccharomyces cerevisiae

Reaction

EC Number Reaction Comment Organism Reaction ID
1.1.1.42 isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH + H+ active site structure and reaction mechanism, conformational changes at the active site resulting in closed and open forms, regulatory residues are isocitrate-binding Asp279and Ser94 Homo sapiens
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.1.1.42 D-isocitrate + NADP+ the reaction is reversible for isozyme IDP2 Saccharomyces cerevisiae 2-oxoglutarate + CO2 + NADPH
-
 r
1.1.1.42 isocitrate + NADP+
-
 Homo sapiens 2-oxoglutarate + CO2 + NADPH + H+
-
 ?
1.1.1.42 isocitrate + NADP+ enzyme has a self-regulatory mechanism of activity mimicking the phosphorylation mechanism of bacterial enzymes Homo sapiens 2-oxoglutarate + CO2 + NADPH + H+
-
 ?

Subunits

EC Number Subunits Comment Organism
1.1.1.42 ? x * 46381, isozyme IDP1, mass spectrometry, x * 46562, isozyme IDP2, mass spectrometry, x * 47856, isozyme IDP3, mass spectrometry Saccharomyces cerevisiae
1.1.1.42 More enzyme has 3 different conformational stages Homo sapiens

Synonyms

EC Number Synonyms Comment Organism
1.1.1.42 IDP
-
 Saccharomyces cerevisiae
1.1.1.42 NADP-dependent isocitrate dehydrogenase
-
 Homo sapiens
1.1.1.42 NADP-dependent isocitrate dehydrogenase
-
 Saccharomyces cerevisiae
1.1.1.42 NADP-IDH
-
 Homo sapiens

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
1.1.1.42 6.5
-
 assay at, reverse reaction Saccharomyces cerevisiae
1.1.1.42 7.4
-
 assay at Homo sapiens
1.1.1.42 7.5
-
 isozyme IDP2, forward reaction Saccharomyces cerevisiae
1.1.1.42 8
-
 isozyme IDP1, forward reaction Saccharomyces cerevisiae

pH Range

EC Number pH Minimum pH Maximum Comment Organism
1.1.1.42 6 9.5
-
 Saccharomyces cerevisiae

Cofactor

EC Number Cofactor Comment Organism Structure
1.1.1.42 NADP+
-
 Saccharomyces cerevisiae
1.1.1.42 NADP+ binding site structure, interaction with the 2'-phosphate group of the ribose moiety Homo sapiens
1.1.1.42 NADPH
-
 Saccharomyces cerevisiae

pI Value

EC Number Organism Comment pI Value Maximum pI Value
1.1.1.42 Saccharomyces cerevisiae isozyme IDP2
-
 5.5
1.1.1.42 Saccharomyces cerevisiae isozyme IDP1
-
 8.5
1.1.1.42 Saccharomyces cerevisiae isozyme IDP3
-
 10