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Literature summary extracted from

  • Wang, P.; Wang, Y.; Guo, X.; Huang, S.; Zhu, G.
    Biochemical and phylogenetic characterization of a monomeric isocitrate dehydrogenase from a marine methanogenic archaeon Methanococcoides methylutens (2020), Extremophiles, 24, 319-328 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.1.1.42 expressed in Escherichia coli Rosetta (DE3) cells Methanococcoides methylutens

Protein Variants

EC Number Protein Variants Comment Organism
1.1.1.42 H590L/R601D the mutant with strongly decreased activity wit NADP+ compared to the wild type enzyme displays a 0.183fold preference for NAD+ over NADP+ Methanococcoides methylutens
1.1.1.42 H590L/R601D/R650S the mutant with severely decreased activity with NADP+ compared to the wild type enzyme displays a 5.93fold preference for NAD+ over NADP+ Methanococcoides methylutens

Inhibitors

EC Number Inhibitors Comment Organism Structure
1.1.1.42 Ca2+ in the presence of Mn2+, Ca2+ strongly inhibits the activity of the enzyme (28.52% residual activity) Methanococcoides methylutens
1.1.1.42 Zn2+ in the presence of Mn2+, Zn2+ strongly inhibits the activity of the enzyme (42.59% residual activity) Methanococcoides methylutens

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
1.1.1.42 0.0168
-
 NADP+ wild type enzyme, in the presence of Mn2+, at pH 8.2 and 45°C Methanococcoides methylutens
1.1.1.42 0.4868
-
 NADP+ mutant enzyme H590L/R601D, in the presence of Mn2+, at pH 8.2 and 45°C Methanococcoides methylutens
1.1.1.42 2.62
-
 NAD+ mutant enzyme H590L/R601D, in the presence of Mn2+, at pH 8.2 and 45°C Methanococcoides methylutens
1.1.1.42 3.474
-
 NAD+ mutant enzyme H590L/R601D/R650S, in the presence of Mn2+, at pH 8.2 and 45°C Methanococcoides methylutens
1.1.1.42 10.457
-
 NADP+ mutant enzyme H590L/R601D/R650S, in the presence of Mn2+, at pH 8.2 and 45°C Methanococcoides methylutens

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
1.1.1.42 Mg2+ Mg2+ can partially replace the activation of Mn2+ (40.3%). 2 mM used in assay conditions Methanococcoides methylutens
1.1.1.42 Mn2+ Mn2+ is the most favored cation, 2 mM used in assay conditions Methanococcoides methylutens
1.1.1.42 additional information Ni2+, Co2+, Na+, K+ and Li+ have almost no effect on the activity of the enzyme when assayed in the presence of Mn2+ Methanococcoides methylutens

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+ Methanococcoides methylutens
-
 2-oxoglutarate + CO2 + NADPH + H+
-
 ?
1.1.1.42 isocitrate + NADP+ Methanococcoides methylutens MM1
-
 2-oxoglutarate + CO2 + NADPH + H+
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
1.1.1.42 Methanococcoides methylutens A0A0E3SSZ6
-
-
1.1.1.42 Methanococcoides methylutens MM1 A0A0E3SSZ6
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.1.1.42 Co2+ affinity resin column chromatography Methanococcoides methylutens

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.1.1.42 isocitrate + NAD+ the reaction is catalyzed by mutant enzymes H590L/R601D/R650S and H590L/R601D Methanococcoides methylutens 2-oxoglutarate + CO2 + NADH + H+
-
 ?
1.1.1.42 isocitrate + NAD+ the reaction is catalyzed by mutant enzymes H590L/R601D/R650S and H590L/R601D Methanococcoides methylutens MM1 2-oxoglutarate + CO2 + NADH + H+
-
 ?
1.1.1.42 isocitrate + NADP+
-
 Methanococcoides methylutens 2-oxoglutarate + CO2 + NADPH + H+
-
 ?
1.1.1.42 isocitrate + NADP+
-
 Methanococcoides methylutens MM1 2-oxoglutarate + CO2 + NADPH + H+
-
 ?
1.1.1.42 additional information the enzyme is highly specific to NADP+ and cannot utilize NAD+ Methanococcoides methylutens ?
-
-
1.1.1.42 additional information the enzyme is highly specific to NADP+ and cannot utilize NAD+ Methanococcoides methylutens MM1 ?
-
-

Subunits

EC Number Subunits Comment Organism
1.1.1.42 monomer 1 * 80000, SDS-PAGE Methanococcoides methylutens
1.1.1.42 monomer 1 * 81000, calculated from amino acid sequence Methanococcoides methylutens

Synonyms

EC Number Synonyms Comment Organism
1.1.1.42 IDH
-
 Methanococcoides methylutens

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
1.1.1.42 45
-
 with Mn2+ Methanococcoides methylutens
1.1.1.42 50
-
 with Mg2+ Methanococcoides methylutens

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
1.1.1.42 35 39 the enzyme is stable below 35°C. The enzyme sustains 50% activity after incubation at 39°C for 20 min with Mn2+ and 38°C with Mg2+ Methanococcoides methylutens

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1.1.1.42 52.3
-
 NAD+ mutant enzyme H590L/R601D, in the presence of Mn2+, at pH 8.2 and 45°C Methanococcoides methylutens
1.1.1.42 53.1
-
 NADP+ mutant enzyme H590L/R601D, in the presence of Mn2+, at pH 8.2 and 45°C Methanococcoides methylutens
1.1.1.42 55.5
-
 NADP+ wild type enzyme, in the presence of Mn2+, at pH 8.2 and 45°C Methanococcoides methylutens
1.1.1.42 57.9
-
 NADP+ mutant enzyme H590L/R601D/R650S, in the presence of Mn2+, at pH 8.2 and 45°C Methanococcoides methylutens
1.1.1.42 113.9
-
 NAD+ mutant enzyme H590L/R601D/R650S, in the presence of Mn2+, at pH 8.2 and 45°C Methanococcoides methylutens

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
1.1.1.42 8.2
-
 with Mn2+ Methanococcoides methylutens
1.1.1.42 8.5
-
 with Mg2+ Methanococcoides methylutens

Cofactor

EC Number Cofactor Comment Organism Structure
1.1.1.42 NADP+ the enzyme is highly specific for NADP+ Methanococcoides methylutens

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 0.00553
-
 NADP+ mutant enzyme H590L/R601D/R650S, in the presence of Mn2+, at pH 8.2 and 45°C Methanococcoides methylutens
1.1.1.42 0.01996
-
 NAD+ mutant enzyme H590L/R601D, in the presence of Mn2+, at pH 8.2 and 45°C Methanococcoides methylutens
1.1.1.42 0.03278
-
 NAD+ mutant enzyme H590L/R601D/R650S, in the presence of Mn2+, at pH 8.2 and 45°C Methanococcoides methylutens
1.1.1.42 0.109
-
 NADP+ mutant enzyme H590L/R601D, in the presence of Mn2+, at pH 8.2 and 45°C Methanococcoides methylutens
1.1.1.42 3.303
-
 NADP+ wild type enzyme, in the presence of Mn2+, at pH 8.2 and 45°C Methanococcoides methylutens