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Literature summary extracted from
- Biochemical characterization and complete conversion of coenzyme specificity of isocitrate dehydrogenase from bifidobacterium longum (2016), Int. J. Mol. Sci., 17, 296.
Cloned(Commentary)
| EC Number | Cloned (Comment) | Organism |
|---|---|---|
| 1.1.1.42 | gene icd, phylogenetic analysis, recombinant expression of His6-tagged enzyme in Escherichia coli strain Rosetta (DE3) | Bifidobacterium longum subsp. infantis |
Protein Variants
| EC Number | Protein Variants | Comment | Organism |
|---|---|---|---|
| 1.1.1.42 | D253A/S257K/K260Q/R314D/H315I/T327A | site-directed mutagenesis, the mutant shows a witch in cofactor specificity from NADP+ to NAD+ | Bifidobacterium longum subsp. infantis |
| 1.1.1.42 | additional information | the coenzyme specificity of BlIDH can be completely reversed from NADP+ to NAD+ by a factor of 2387 by replacing six residues. The loss in NADP+-dependent activity might result from the removal of favorable interactions between Arg314 or His315 and the 2'-phosphate group | Bifidobacterium longum subsp. infantis |
| 1.1.1.42 | R314D | site-directed mutagenesis | Bifidobacterium longum subsp. infantis |
| 1.1.1.42 | R314D/H315I/T327A | site-directed mutagenesis | Bifidobacterium longum subsp. infantis |
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 analysis, overview | Bifidobacterium longum subsp. infantis | |
| 1.1.1.42 | 0.01945 | - |
NADP+ | pH 8.0, 25°C, recombinant wild-type enzyme | Bifidobacterium longum subsp. infantis |  |
| 1.1.1.42 | 0.13 | - |
NAD+ | pH 8.0, 25°C, recombinant mutant D253A/S257K/K260Q/R314D/H315I/T327A | Bifidobacterium longum subsp. infantis | |
| 1.1.1.42 | 0.324 | - |
NADP+ | pH 8.0, 25°C, recombinant mutant D253A/S257K/K260Q/R314D/H315I/T327A | Bifidobacterium longum subsp. infantis | |
| 1.1.1.42 | 3.58 | - |
NAD+ | pH 8.0, 25°C, recombinant wild-type enzyme | Bifidobacterium longum subsp. infantis | |
Metals/Ions
| EC Number | Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|---|
| 1.1.1.42 | Co2+ | 14.3% activity compared to Mn2+ | Bifidobacterium longum subsp. infantis | |
| 1.1.1.42 | Mg2+ | 69.2% activity compared to Mn2+ | Bifidobacterium longum subsp. infantis | |
| 1.1.1.42 | Mn2+ | best activating cation | Bifidobacterium longum subsp. infantis | |
| 1.1.1.42 | additional information | the enzyme is dependent on divalent cations, overview. No activity with Zn2+, Cu2+, Ca2+, and Li+,very low activity with K+, Na+, Ni2+, and Rb+ | Bifidobacterium longum subsp. infantis |
Molecular Weight [Da]
| EC Number | Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|---|
| 1.1.1.42 | 45000 | - |
- |
Bifidobacterium longum subsp. infantis |
| 1.1.1.42 | 83000 | - |
recombinant His6-tagged enzyme, gel filtration | Bifidobacterium longum subsp. infantis |
Natural Substrates/ Products (Substrates)
| EC Number | Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 1.1.1.42 | isocitrate + NADP+ | Bifidobacterium longum subsp. infantis | - |
2-oxoglutarate + CO2 + NADPH + H+ | - |
r | |
| 1.1.1.42 | isocitrate + NADP+ | Bifidobacterium longum subsp. infantis ATCC 15697 | - |
2-oxoglutarate + CO2 + NADPH + H+ | - |
r | |
Organism
| EC Number | Organism | UniProt | Comment | Textmining |
|---|---|---|---|---|
| 1.1.1.42 | Bifidobacterium longum subsp. infantis | B7GQR3 | - |
- |
| 1.1.1.42 | Bifidobacterium longum subsp. infantis ATCC 15697 | B7GQR3 | - |
- |
Purification (Commentary)
| EC Number | Purification (Comment) | Organism |
|---|---|---|
| 1.1.1.42 | recombinant His6-tagged enzyme from Escherichia coli strain Rosetta (DE3) by Co2+ affinity chromatography | Bifidobacterium longum subsp. infantis |
Substrates and Products (Substrate)
| EC Number | Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 1.1.1.42 | isocitrate + NAD+ | engineered enzyme mutant D253A/S257K/K260Q/R314D/H315I/T327A, cf. EC 1.1.1.41 | Bifidobacterium longum subsp. infantis | 2-oxoglutarate + CO2 + NADH + H+ | - |
r | |
| 1.1.1.42 | isocitrate + NAD+ | engineered enzyme mutant D253A/S257K/K260Q/R314D/H315I/T327A, cf. EC 1.1.1.41 | Bifidobacterium longum subsp. infantis ATCC 15697 | 2-oxoglutarate + CO2 + NADH + H+ | - |
r | |
| 1.1.1.42 | isocitrate + NADP+ | - |
Bifidobacterium longum subsp. infantis | 2-oxoglutarate + CO2 + NADPH + H+ | - |
r | |
| 1.1.1.42 | isocitrate + NADP+ | - |
Bifidobacterium longum subsp. infantis ATCC 15697 | 2-oxoglutarate + CO2 + NADPH + H+ | - |
r | |
Subunits
| EC Number | Subunits | Comment | Organism |
|---|---|---|---|
| 1.1.1.42 | homodimer | 2 * 45000, recombinant His6-tagged enzyme, SDS-PAGE | Bifidobacterium longum subsp. infantis |
Synonyms
| EC Number | Synonyms | Comment | Organism |
|---|---|---|---|
| 1.1.1.42 | ICD | - |
Bifidobacterium longum subsp. infantis |
| 1.1.1.42 | NADP+-dependent IDH | - |
Bifidobacterium longum subsp. infantis |
| 1.1.1.42 | NADP-IDH | - |
Bifidobacterium longum subsp. infantis |
Temperature Optimum [°C]
| EC Number | Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|---|
| 1.1.1.42 | 60 | - |
with Mn2+ | Bifidobacterium longum subsp. infantis |
| 1.1.1.42 | 65 | - |
with Mg2+ | Bifidobacterium longum subsp. infantis |
Temperature Stability [°C]
| EC Number | Temperature Stability Minimum [°C] | Temperature Stability Maximum [°C] | Comment | Organism |
|---|---|---|---|---|
| 1.1.1.42 | 45 | - |
enzyme BlIDH retains 50% of maximal activity after incubation at 45°C for 20 min with either Mn2+ or Mg2+ | Bifidobacterium longum subsp. infantis |
Turnover Number [1/s]
| EC Number | Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|---|
| 1.1.1.42 | 0.307 | - |
NADP+ | pH 8.0, 25°C, recombinant mutant D253A/S257K/K260Q/R314D/H315I/T327A | Bifidobacterium longum subsp. infantis | |
| 1.1.1.42 | 0.518 | - |
NAD+ | pH 8.0, 25°C, recombinant mutant D253A/S257K/K260Q/R314D/H315I/T327A | Bifidobacterium longum subsp. infantis | |
| 1.1.1.42 | 11.7 | - |
NAD+ | pH 8.0, 25°C, recombinant wild-type enzyme | Bifidobacterium longum subsp. infantis | |
| 1.1.1.42 | 36.4 | - |
NADP+ | pH 8.0, 25°C, recombinant wild-type enzyme | Bifidobacterium longum subsp. infantis | |
pH Optimum
| EC Number | pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|---|
| 1.1.1.42 | 7.5 | - |
with Mn2+ | Bifidobacterium longum subsp. infantis |
| 1.1.1.42 | 8 | - |
with Mg2+ | Bifidobacterium longum subsp. infantis |
Cofactor
| EC Number | Cofactor | Comment | Organism | Structure |
|---|---|---|---|---|
| 1.1.1.42 | additional information | the enzyme shows a 567 and 193fold preference for NADP+ over NAD+ in the presence of Mg2+ and Mn2+, respectively. The coenzyme specificity of BlIDH can be completely reversed from NADP+ to NAD+ by a factor of 2387 by replacing six residues by rational mutagenesis | Bifidobacterium longum subsp. infantis | |
| 1.1.1.42 | NADP+ | - |
Bifidobacterium longum subsp. infantis | |
| 1.1.1.42 | NADPH | - |
Bifidobacterium longum subsp. infantis | |
General Information
| EC Number | General Information | Comment | Organism |
|---|---|---|---|
| 1.1.1.42 | evolution | based on the phylogenetic analysis, IDHs can be divided into three subfamilies: Type I IDHs, Type II IDHs and monomeric IDHs. The enzyme BlIDH from Bifidobacterium longum belongs to the type II subfamily. NAD+ use is an ancestral trait and NADP+ use by bacterial IDHs arose on or about the time that eukaryotic mitochondria first appeared, some 3.5 billion years ago | Bifidobacterium longum subsp. infantis |
| 1.1.1.42 | physiological function | NADP+-dependent IDH generates NADPH, which provides the reducing power for biosynthesis, maintains the redox state of the cell, and takes part in CO2 assimilation | Bifidobacterium longum subsp. infantis |
kcat/KM [mM/s]
| EC Number | kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|---|
| 1.1.1.42 | 0.95 | - |
NAD+ | pH 8.0, 25°C, recombinant mutant D253A/S257K/K260Q/R314D/H315I/T327A | Bifidobacterium longum subsp. infantis | |
| 1.1.1.42 | 3 | - |
NAD+ | pH 8.0, 25°C, recombinant wild-type enzyme | Bifidobacterium longum subsp. infantis | |
| 1.1.1.42 | 4 | - |
NAD+ | pH 8.0, 25°C, recombinant mutant D253A/S257K/K260Q/R314D/H315I/T327A | Bifidobacterium longum subsp. infantis | |
| 1.1.1.42 | 1870 | - |
NAD+ | pH 8.0, 25°C, recombinant wild-type enzyme | Bifidobacterium longum subsp. infantis | |
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