1.1.1.42: isocitrate dehydrogenase (NADP+)

This is an abbreviated version, for detailed information about isocitrate dehydrogenase (NADP+), go to the full flat file.

Reaction

isocitrate
+
NADP+
=
2-oxoglutarate
+
CO2
+
NADPH
+
H+

Synonyms

AfIDH, CgIDH, cICDH, CtIDP1, CtIDP2, cytosolic isocitrate dehydrogenase 1, cytosolic NADP(+)-dependent isocitrate dehydrogenase, cytosolic NADP+-dependent isocitrate dehydrogenase, cytosolic NADP-dependent isocitrate dehydrogenase, cytosolic NADPH-dependent isocitrate dehydrogenase, DpIDH, EcIDH, ICD, ICD1, ICD2, ICDH, ICDH-1, IDH, IDH1, IDH2, IDH3, IDHP, IDP, IDP1, IDP2, IDP3, IDPA, IDPc, IDPm, isocitrate dehydrogenase, isocitrate dehydrogenase (NADP), isocitrate dehydrogenase (NADP-dependent), isocitrate dehydrogenase (nicotinamide adenine dinucleotide phosphate), isocitrate dehydrogenase 1, isocitrate dehydrogenase 2, isocitrate dehydrogenase-1, isocytrate deyhdrogenase, mICDH, mitochondrial NADP+-dependent isocitrate dehydrogenase, NAD+-dependent isocitrate dehydrogenase, NADP isocitric dehydrogenase, NADP+-dependent Ds-threo-isocitrate dehydrogenase, NADP+-dependent Ds-threo-isocitrate:NADP+ oxidoreductase, NADP+-dependent IDH, NADP+-dependent isocitrate dehydrogenase, NADP+-ICDH, NADP+-IDH, NADP+-isocitrate dehydrogenase, NADP+-linked isocitrate dehydrogenase, NADP+-specific ICDH, NADP+-specific isocitrate dehydrogenase, NADP-dependent IDH, NADP-dependent isocitrate dehydrogenase, NADP-dependent isocitric dehydrogenase, NADP-ICDH, NADP-IDH, NADP-IDH Idp1p, NADP-isocitrate dehydrogenase, NADP-linked isocitrate dehydrogenase, NADP-specific isocitrate dehydrogenase, NADPH-dependent isocitrate dehydrogenase, oxalosuccinate decarboxylase, oxalsuccinic decarboxylase, perICDH, PS-NADP-IDH, TaIDH, TM1148

ECTree

     1 Oxidoreductases
         1.1 Acting on the CH-OH group of donors
             1.1.1 With NAD+ or NADP+ as acceptor
                1.1.1.42 isocitrate dehydrogenase (NADP+)

Crystallization

Crystallization on EC 1.1.1.42 - isocitrate dehydrogenase (NADP+)

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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystal structures of a native enzyme at 2.2 A, a pseudo-native enzyme at 2.1 A, and of the enzyme in complex with NADP+, Ca2+ and D-isocitrate at 2.3 A
-
crystallization is carried out by the hanging-drop method at 20°C
-
hanging drop vapour diffusion technique with reservoir solution consisting of 0.6 M ZnSO4 and 0.1 M Na cacodylate, pH 6.3
-
crystallization with polyethylene glycol 2000 monomethyl ether
-
hanging drop vapour diffusion method, 0.001 ml of 10 mg/ml protein in 12.5 mM 2-morpholinoethanesulfonic acid, pH 6.2, with 1.25 mM MnSO4, 1.25 mM dithiothreitol and 10% glycerol, is mixed with 0.001 ml of reservoir solution containing 25% w/v PEG 2000 MME, 0.2 M Tris-HCl, pH 7.3, and 0.2 M MgCl2, and with or without 0.001 ml of 10 mM NADP+, 3 days to 2 months, X-ray diffrcation structure determination and analysis at 1.8-1.9 A resolution, molecular replacement
substrate/cofactor-free structure in presence of Mg2+ shows a distinct open conformation and suggests the presence of low-energy conformers
-
crystals of native DpIDH are obtained by the sitting-drop, vapour-diffusion method. The crystals are grown at 8°C. Crystals of DpIDH in complex with isocitrate (DpIDH-iso) are obtained by the hanging drop method at 8 °C
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
-
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
crystal structures of Saccharomyces cerevesiae mitochondrial NADP-IDH Idp1p in binary complexes with coenzyme NADP+, or substrate isocitrate, or product 2-oxoglutarate, and in a quaternary complex with NADPH, 2-oxoglutarate, and Ca2+, which represent different enzymatic states during the catalytic reaction. Crystallization is carried out at 20°C using the hanging-drop vapor diffusion method
-
20 mg/ml purified recombinant wild-type and selenomethionine enzyme, complexed with Mn2+ and isocitrate, 4°C, hanging drop vapour diffusion method, for the wild-type enzyme: 0.002 ml of enzyme solution containing 0.1 M triethanolamine chloride, pH 7.7, 0.15 M Na2SO4, 8 mM DL-isocitrate, 4 mM MnSO4, plus equal volume of 20% PEG 6000, 3% glycerol, against 0.75 ml reservoir solution containing 0.1 M triethanolamine chloride, pH 7.7, 0.15 M Na2SO4, 8 mM DL-isocitrate, 4 mM MnSO4, and 40% w/v xylitol, for the selenomethionine enzyme: 0.002 ml of enzyme solution containing 0.1 M triethanolamine chloride, pH 7.7, 0.15 M Na2SO4, 8 mM DL-isocitrate, plus equal volume of 18% PEG 6000, 3% glycerol, against 0.75 ml reservoir solution containing 0.1 M triethanolamine chloride, pH 7.7, 0.15 M Na2SO4, and 18% PEG 6000, 7-10 days, X-ray diffraction structure determination and analysis at 2.7 A resolution, modeling
-
in complex with Mn2+ and isocitrate
-
dimeric apoform
-
sitting and hanging drop vapour diffusion method, using 100 mM cacodylate and 1.4 M sodium acetate, 10 mM citric acid , and 10 mM MnCl2, at pH 6.5-7.8 and 25°C