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Literature summary extracted from

  • Lv, P.; Tang, W.; Wang, P.; Cao, Z.; Zhu, G.
    Enzymatic characterization and functional implication of two structurally different isocitrate dehydrogenases from Xylella fastidiosa (2018), Biotechnol. Appl. Biochem., 65, 230-237 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.1.1.41 expressed in Escherichia coli Rosetta(DE3) cells Xylella fastidiosa
1.1.1.42 expressed in Escherichia coli Rosetta(DE3) cells Xylella fastidiosa

Protein Variants

EC Number Protein Variants Comment Organism
1.1.1.41 D268K the coenzyme specificity of the mutant is switched from NAD+ to NADP+ Xylella fastidiosa
1.1.1.41 D268K/I269Y the coenzyme specificity of the mutant is switched from NAD+ to NADP+ Xylella fastidiosa
1.1.1.41 D268K/I269Y/A275V the coenzyme specificity of the mutant is switched from NAD+ to NADP+ Xylella fastidiosa
1.1.1.42 H590L/R601L the mutations greatly reduce the affinity for NADP+, but fail to improve the ability to use NAD+ so the mutant has similar affinities to NADP+ and NAD+ Xylella fastidiosa
1.1.1.42 K589T/H590L/R601L the mutations greatly reduce the affinity for NADP+, but fail to improve the ability to use NAD+ so the mutant has similar affinities to NADP+ and NAD+ Xylella fastidiosa

Inhibitors

EC Number Inhibitors Comment Organism Structure
1.1.1.41 Ca2+ 7.9% residual activity at 2 mM Xylella fastidiosa
1.1.1.41 Co2+ 5.2% residual activity at 2 mM Xylella fastidiosa
1.1.1.41 Cu2+ complete inhibition at 2 mM Xylella fastidiosa
1.1.1.41 K+ complete inhibition at 2 mM Xylella fastidiosa
1.1.1.41 Na+ complete inhibition at 2 mM Xylella fastidiosa
1.1.1.41 Ni2+ complete inhibition at 2 mM Xylella fastidiosa
1.1.1.41 Zn2+ complete inhibition at 2 mM Xylella fastidiosa
1.1.1.42 Ca2+ 3.0% residual activity at 2 mM Xylella fastidiosa
1.1.1.42 Co2+ 8.9% residual activity at 2 mM Xylella fastidiosa
1.1.1.42 Cu2+ complete inhibition at 2 mM Xylella fastidiosa
1.1.1.42 K+ 3.9% residual activity at 2 mM Xylella fastidiosa
1.1.1.42 Na+ 5.2% residual activity at 2 mM Xylella fastidiosa
1.1.1.42 Ni2+ 3.8% residual activity at 2 mM Xylella fastidiosa
1.1.1.42 Zn2+ complete inhibition at 2 mM Xylella fastidiosa

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
1.1.1.41 0.031
-
 NADP+ mutant enzymeD268K/I269Y/A275V, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 0.087
-
 NADP+ mutant enzyme D268K/I269Y, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 0.101
-
 NADP+ mutant enzyme D268K, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 0.121
-
 NAD+ wild type enzyme, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 0.384
-
 NAD+ mutant enzyme D268K, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 2.339
-
 NADP+ wild type enzyme, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 3.15
-
 NAD+ mutant enzymeD268K/I269Y/A275V, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 4.413
-
 NAD+ mutant enzyme D268K/I269Y, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.42 0.001
-
 NAD+ wild type enzyme, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.42 0.959
-
 NAD+ mutant enzyme K589T/H590L/R601L, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.42 1.506
-
 NAD+ mutant enzyme H590L/R601L, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.42 2.455
-
 NAD+ wild type enzyme, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.42 2.695
-
 NAD+ mutant enzyme H590L/R601L, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.42 5.534
-
 NAD+ mutant enzyme K589T/H590L/R601L, at pH 8.0 and 25°C Xylella fastidiosa

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
1.1.1.41 Mg2+ Mg2+ is the most favored divalent cation. Mg2+ can be largely replaced by Mn2+ (69.2% activity). 2 mM is used in assay conditions Xylella fastidiosa
1.1.1.42 Mn2+ Mn2+ is the most favored divalent cation. Mn2+ can be partly replaced by Mg2+ (17.6% activity). 2 mM is used in assay conditions Xylella fastidiosa

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
1.1.1.41 75500
-
 MALDI-TOF mass spectrometry Xylella fastidiosa
1.1.1.42 82400
-
 MALDI-TOF mass spectrometry Xylella fastidiosa

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+ Xylella fastidiosa
-
 2-oxoglutarate + CO2 + NADH + H+
-
 ?
1.1.1.42 isocitrate + NADP+ Xylella fastidiosa
-
 2-oxoglutarate + CO2 + NADPH + H+
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
1.1.1.41 Xylella fastidiosa
-
-
-
1.1.1.42 Xylella fastidiosa
-
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.1.1.41 metal affinity resin column chromatography Xylella fastidiosa
1.1.1.42 metal affinity resin column chromatography Xylella fastidiosa

Specific Activity [micromol/min/mg]

EC Number Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
1.1.1.41 6.3
-
 with NADP+ as cosubstrate, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 96.8
-
 with NAD+ as cosubstrate, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.42 7.4
-
 with NAD+ as cosubstrate, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.42 73.2
-
 with NADP+ as cosubstrate, at pH 8.0 and 25°C Xylella fastidiosa

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.1.1.41 isocitrate + NAD+
-
 Xylella fastidiosa 2-oxoglutarate + CO2 + NADH + H+
-
 ?
1.1.1.41 isocitrate + NADP+
-
 Xylella fastidiosa 2-oxoglutarate + CO2 + NADPH + H+
-
 ?
1.1.1.42 isocitrate + NAD+
-
 Xylella fastidiosa 2-oxoglutarate + CO2 + NADH + H+
-
 ?
1.1.1.42 isocitrate + NADP+
-
 Xylella fastidiosa 2-oxoglutarate + CO2 + NADPH + H+
-
 ?

Subunits

EC Number Subunits Comment Organism
1.1.1.41 homodimer 2 * 38000, SDS-PAGE Xylella fastidiosa
1.1.1.42 monomer 1 * 80000, SDS-PAGE Xylella fastidiosa

Synonyms

EC Number Synonyms Comment Organism
1.1.1.41 NAD+-dependent IDH
-
 Xylella fastidiosa
1.1.1.41 NADH-IDH
-
 Xylella fastidiosa
1.1.1.42 NADP+-dependent IDH
-
 Xylella fastidiosa
1.1.1.42 NADPH-IDH
-
 Xylella fastidiosa

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
1.1.1.41 55
-
-
 Xylella fastidiosa
1.1.1.42 50
-
-
 Xylella fastidiosa

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
1.1.1.41 40 47 the enzyme is stable below 40°C and half of its activity is lost after incubation at 47°C for 20 min Xylella fastidiosa
1.1.1.42 35 42 the enzyme is stable below 35°C, but its activity decreases rapidly above 35°C. The enzyme is almost inactivated after incubation at 42.5°C for 20 min Xylella fastidiosa

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1.1.1.41 6.1
-
 NADP+ wild type enzyme, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 6.9
-
 NADP+ mutant enzymeD268K/I269Y/A275V, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 11.8
-
 NAD+ mutant enzymeD268K/I269Y/A275V, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 30.4
-
 NADP+ mutant enzyme D268K/I269Y, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 37.3
-
 NAD+ mutant enzyme D268K/I269Y, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 38.5
-
 NADP+ mutant enzyme D268K, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 52.8
-
 NAD+ mutant enzyme D268K, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 74.6
-
 NAD+ wild type enzyme, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.42 8.9
-
 NAD+ mutant enzyme K589T/H590L/R601L, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.42 16.7
-
 NAD+ wild type enzyme, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.42 30.8
-
 NAD+ mutant enzyme H590L/R601L, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.42 56.1
-
 NAD+ mutant enzyme K589T/H590L/R601L, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.42 62.4
-
 NAD+ mutant enzyme H590L/R601L, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.42 96.5
-
 NAD+ wild type enzyme, at pH 8.0 and 25°C Xylella fastidiosa

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
1.1.1.41 8 9 the enzyme retains more than 95% activity at pH 8.0-9.0 with Mg2+ Xylella fastidiosa
1.1.1.42 7.8
-
 in the presence of Mn2+ Xylella fastidiosa

Cofactor

EC Number Cofactor Comment Organism Structure
1.1.1.41 NAD+ the enzyme displays 206fold preferences for NAD+ over NADP+ Xylella fastidiosa
1.1.1.42 NADP+ the enzyme shows 13800fold preferences for NADP+ over NAD+ Xylella fastidiosa

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
-
 NADP+ wild type enzyme, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 4
-
 NAD+ mutant enzymeD268K/I269Y/A275V, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 8
-
 NAD+ mutant enzyme D268K/I269Y, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 138
-
 NAD+ mutant enzyme D268K, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 223
-
 NADP+ mutant enzymeD268K/I269Y/A275V, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 349
-
 NADP+ mutant enzyme D268K/I269Y, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 381
-
 NADP+ mutant enzyme D268K, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.41 617
-
 NAD+ wild type enzyme, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.42 7
-
 NAD+ wild type enzyme, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.42 9
-
 NAD+ mutant enzyme K589T/H590L/R601L, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.42 10
-
 NAD+ mutant enzyme K589T/H590L/R601L, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.42 20
-
 NAD+ mutant enzyme H590L/R601L, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.42 23
-
 NAD+ mutant enzyme H590L/R601L, at pH 8.0 and 25°C Xylella fastidiosa
1.1.1.42 96500
-
 NAD+ wild type enzyme, at pH 8.0 and 25°C Xylella fastidiosa