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Literature summary extracted from
- A unique homodimeric NAD+-linked isocitrate dehydrogenase from the smallest autotrophic eukaryote Ostreococcus tauri (2015), FASEB J., 29, 2462-2472.
Cloned(Commentary)
| EC Number | Cloned (Comment) | Organism |
|---|---|---|
| 1.1.1.41 | DNA and amino acid sequence determination and analysis, phylogenetic tree, recombinant expression of His6-tagged wild-type and mutant enzymes in Escherichia coli strain Rosetta (DE3) | Ostreococcus tauri |
Protein Variants
| EC Number | Protein Variants | Comment | Organism |
|---|---|---|---|
| 1.1.1.41 | D344R | site-directed mutagenesis, the mutant enzyme retains their native dimeric structure, and the mutant displays a 15fold preference for NADP+ over NAD+ compared to the wild-type enzyme | Ostreococcus tauri |
| 1.1.1.41 | D344R/M345H | site-directed mutagenesis, the mutant enzyme retains their native dimeric structure, the mutant displays a 72fold preference for NADP+ over NAD+ compared to the wild-type enzyme | Ostreococcus tauri |
| 1.1.1.41 | additional information | the enzyme's coenzyme specificity can be completely converted from NAD+ (ancient trait) to NADP+ (adaptive trait) by rational mutagenesis based on the evolutionary trace. Residues D344 and M345 are the determinants of NAD+ specificity | Ostreococcus tauri |
Inhibitors
| EC Number | Inhibitors | Comment | Organism | Structure |
|---|---|---|---|---|
| 1.1.1.41 | 2-oxoglutarate | strong inhibition at 10 mM | Ostreococcus tauri |  |
| 1.1.1.41 | ATP | strong inhibition at 10 mM | Ostreococcus tauri | |
| 1.1.1.41 | additional information | no inhibition by NADPH and citrate | Ostreococcus tauri | |
| 1.1.1.41 | NADH | comptitive with respect to NAD+ | Ostreococcus tauri | |
KM Value [mM]
| EC Number | KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|---|
| 1.1.1.41 | additional information | - |
additional information | OtIDH exhibits a sigmoidal kinetic behavior in response to isocitrate unlike other homodimeric enzyme homologues, and a remarkably high affinity for isocitrate unlike other heterooligomeric enzyme homologues | Ostreococcus tauri | |
| 1.1.1.41 | 0.0139 | - |
NADP+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant mutant D344R/M345H, with Mn2+ | Ostreococcus tauri | |
| 1.1.1.41 | 0.067 | - |
NADP+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant mutant D344R, with Mn2+ | Ostreococcus tauri | |
| 1.1.1.41 | 0.226 | - |
NAD+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant wild-type enzyme, with Mn2+ | Ostreococcus tauri | |
| 1.1.1.41 | 0.265 | - |
NAD+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant wild-type enzyme, with Mg2+ | Ostreococcus tauri | |
| 1.1.1.41 | 0.738 | - |
NAD+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant mutant D344R, with Mn2+ | Ostreococcus tauri | |
| 1.1.1.41 | 3.354 | - |
NADP+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant wild-type enzyme, with Mg2+ | Ostreococcus tauri | |
| 1.1.1.41 | 4.314 | - |
NADP+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant wild-type enzyme, with Mn2+ | Ostreococcus tauri | |
| 1.1.1.41 | 20.65 | - |
NAD+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant mutant D344R/M345H, with Mn2+ | Ostreococcus tauri | |
Localization
| EC Number | Localization | Comment | Organism | GeneOntology No. | Textmining |
|---|---|---|---|---|---|
| 1.1.1.41 | mitochondrion | resticted to | Ostreococcus tauri | 5739 | - |
Metals/Ions
| EC Number | Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|---|
| 1.1.1.41 | Mg2+ | activates | Ostreococcus tauri | |
| 1.1.1.41 | Mn2+ | activates | Ostreococcus tauri | |
Molecular Weight [Da]
| EC Number | Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|---|
| 1.1.1.41 | 46700 | - |
- |
Ostreococcus tauri |
| 1.1.1.41 | 93000 | - |
about, sequence calculation | Ostreococcus tauri |
| 1.1.1.41 | 108000 | - |
recombinant His6-tagged enzyme, gel filtration | Ostreococcus tauri |
Natural Substrates/ Products (Substrates)
| EC Number | Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 1.1.1.41 | isocitrate + NAD+ | Ostreococcus tauri | - |
2-oxoglutarate + CO2 + NADH + H+ | - |
? | |
Organism
| EC Number | Organism | UniProt | Comment | Textmining |
|---|---|---|---|---|
| 1.1.1.41 | Ostreococcus tauri | - |
- |
- |
Purification (Commentary)
| EC Number | Purification (Comment) | Organism |
|---|---|---|
| 1.1.1.41 | recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain Rosetta (DE3) by Co2+ affinity chromatography | Ostreococcus tauri |
Substrates and Products (Substrate)
| EC Number | Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 1.1.1.41 | DL-isocitrate + NAD+ | - |
Ostreococcus tauri | 2-oxoglutarate + CO2 + NADH | - |
? | |
| 1.1.1.41 | DL-isocitrate + NADP+ | very low activity | Ostreococcus tauri | 2-oxoglutarate + CO2 + NADPH | - |
? | |
| 1.1.1.41 | isocitrate + NAD+ | - |
Ostreococcus tauri | 2-oxoglutarate + CO2 + NADH + H+ | - |
? | |
Subunits
| EC Number | Subunits | Comment | Organism |
|---|---|---|---|
| 1.1.1.41 | homodimer | 2 * 47000-49000, recombinant His6-tagged enzyme, SDS-PAGE, 2 * 46700, about, sequence calculation | Ostreococcus tauri |
| 1.1.1.41 | More | comparative protein structure modeling using the mature OtIDH protein sequence, overview | Ostreococcus tauri |
Synonyms
| EC Number | Synonyms | Comment | Organism |
|---|---|---|---|
| 1.1.1.41 | homodimeric NAD+-linked isocitrate dehydrogenase | - |
Ostreococcus tauri |
| 1.1.1.41 | NAD+-dependent isocitrate dehydrogenase | - |
Ostreococcus tauri |
| 1.1.1.41 | NAD-IDH | - |
Ostreococcus tauri |
| 1.1.1.41 | OtIDH | - |
Ostreococcus tauri |
Turnover Number [1/s]
| EC Number | Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|---|
| 1.1.1.41 | 3.9 | - |
NADP+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant mutant D344R/M345H, with Mn2+ | Ostreococcus tauri | |
| 1.1.1.41 | 17 | - |
NADP+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant wild-type enzyme, with Mg2+ | Ostreococcus tauri | |
| 1.1.1.41 | 41 | - |
NAD+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant mutant D344R, with Mn2+ | Ostreococcus tauri | |
| 1.1.1.41 | 46 | - |
NADP+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant wild-type enzyme, with Mn2+ | Ostreococcus tauri | |
| 1.1.1.41 | 56 | - |
NADP+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant mutant D344R, with Mn2+ | Ostreococcus tauri | |
| 1.1.1.41 | 59 | - |
NAD+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant wild-type enzyme, with Mg2+ | Ostreococcus tauri | |
| 1.1.1.41 | 80.9 | - |
NAD+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant mutant D344R/M345H, with Mn2+ | Ostreococcus tauri | |
| 1.1.1.41 | 115 | - |
NAD+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant wild-type enzyme, with Mn2+ | Ostreococcus tauri | |
pH Optimum
| EC Number | pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|---|
| 1.1.1.41 | 7.6 | - |
assay at | Ostreococcus tauri |
Cofactor
| EC Number | Cofactor | Comment | Organism | Structure |
|---|---|---|---|---|
| 1.1.1.41 | additional information | in the presence of Mn2+ and Mg2+, OtIDH displays 42fold and 51fold preference for NAD+ over NADP+, respectively | Ostreococcus tauri | |
| 1.1.1.41 | NAD+ | specific for | Ostreococcus tauri | |
Ki Value [mM]
| EC Number | Ki Value [mM] | Ki Value maximum [mM] | Inhibitor | Comment | Organism | Structure |
|---|---|---|---|---|---|---|
| 1.1.1.41 | 0.14 | - |
NADH | pH 7.6, temperature not specified in the publication, His6-tagged recombinant wild-type enzyme | Ostreococcus tauri | |
General Information
| EC Number | General Information | Comment | Organism |
|---|---|---|---|
| 1.1.1.41 | evolution | OtIDH may be an ancestral form of type II IDHs (all other reported members are NADP+-linked enzymes) and may have evolved into NADP+-dependent IDH for adaptation to the increased demand of NADPH under carbon starvation | Ostreococcus tauri |
| 1.1.1.41 | metabolism | NAD-IDH is a key enzyme in the Krebs cycle | Ostreococcus tauri |
| 1.1.1.41 | additional information | structure homology modelling, overview. Residue Asp344 is clearly a major determinant of coenzyme specificity in OtIDH and residue Met345 plays critical role in NAD+ recognition and binding | Ostreococcus tauri |
kcat/KM [mM/s]
| EC Number | kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|---|
| 1.1.1.41 | 3.9 | - |
NAD+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant mutant D344R/M345H, with Mn2+ | Ostreococcus tauri | |
| 1.1.1.41 | 5.1 | - |
NADP+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant wild-type enzyme, with Mg2+ | Ostreococcus tauri | |
| 1.1.1.41 | 10.7 | - |
NADP+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant wild-type enzyme, with Mn2+ | Ostreococcus tauri | |
| 1.1.1.41 | 55.6 | - |
NAD+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant mutant D344R, with Mn2+ | Ostreococcus tauri | |
| 1.1.1.41 | 261 | - |
NAD+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant wild-type enzyme, with Mg2+ | Ostreococcus tauri | |
| 1.1.1.41 | 281 | - |
NADP+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant mutant D344R/M345H, with Mn2+ | Ostreococcus tauri | |
| 1.1.1.41 | 434 | - |
NAD+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant wild-type enzyme, with Mn2+ | Ostreococcus tauri | |
| 1.1.1.41 | 836 | - |
NADP+ | pH 7.6, temperature not specified in the publication, His6-tagged recombinant mutant D344R, with Mn2+ | Ostreococcus tauri | |
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