BRENDA - Enzyme Database

Chemical mechanism of homoisocitrate dehydrogenase from Saccharomyces cerevisiae

Lin, Y.; Volkman, J.; Nicholas, K.M.; Yamamoto, T.; Eguchi, T.; Nimmo, S.L.; West, A.H.; Cook, P.F.; Biochemistry 47, 4169-4180 (2008)

Data extracted from this reference:

Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
1.1.1.87
3-carboxypropylidenemalate
-
Saccharomyces cerevisiae
1.1.1.87
Mg-homoisocitrate
-
Saccharomyces cerevisiae
1.1.1.286
3-carboxypropylidenemalate
a dead-end inhibitor, competitive versus homoisocitrate
Saccharomyces cerevisiae
1.1.1.286
homoisocitrate
competitive, pH-dependent substrate inhibition
Saccharomyces cerevisiae
1.1.1.286
isocitrate
competitive, pH-dependent substrate inhibition
Saccharomyces cerevisiae
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
1.1.1.87
0.0042
-
Mg-homoisocitrate
oxidate decarboxylation of homoisocitrate
Saccharomyces cerevisiae
1.1.1.87
0.09
-
NADH
reductive carboxylation of alpha-ketoadipate
Saccharomyces cerevisiae
1.1.1.87
0.45
-
NAD+
oxidate decarboxylation of homoisocitrate
Saccharomyces cerevisiae
1.1.1.87
3.2
-
Mg-homoisocitrate
reductive carboxylation of alpha-ketoadipate
Saccharomyces cerevisiae
1.1.1.87
16.3
-
CO2
reductive carboxylation of alpha-ketoadipate
Saccharomyces cerevisiae
1.1.1.286
additional information
-
additional information
kinetic mechanism, detailed overview
Saccharomyces cerevisiae
Metals/Ions
EC Number
Metals/Ions
Commentary
Organism
Structure
1.1.1.87
Mg2+
-
Saccharomyces cerevisiae
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.1.1.286
additional information
Saccharomyces cerevisiae
the enzyme catalyzes the fourth reaction of the alpha-aminoadipate pathway for lysine biosynthesis, the conversion of homoisocitrate to alpha-ketoadipate using NAD+ as an oxidizing agent
?
-
-
-
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
1.1.1.87
Saccharomyces cerevisiae
-
-
-
1.1.1.286
Saccharomyces cerevisiae
-
-
-
Reaction
EC Number
Reaction
Commentary
Organism
1.1.1.87
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD+ = 2-oxoadipate + CO2 + NADH + H+
two enzyme groups act as acid-base catalysts in the reaction. A group with a pKa of 6.5-7 acts as a general base accepting a proton as the beta-hydroxy acid is oxidized to the beta-keto acid, and this residue participates in all three of the chemical steps, acting to shuttle a proton between the C2 hydroxyl and itself. The second group acts as a general acid with a pKa of 9.5 and likely catalyzes the tautomerization step by donating a proton to the enol to give the final product
Saccharomyces cerevisiae
1.1.1.286
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD+ = 2-oxoadipate + CO2 + NADH + H+
chemical mechanism on the basis of the pH dependence of kinetic parameters, dissociation constants for competitive inhibitors, and multiple-substrate deuterium/13C isotope effects suggesting a stepwise mechanism with hydride transfer preceding decarboxylation, the decarboxylation step contributes only slightly to rate limitation, overview
Saccharomyces cerevisiae
1.1.1.286
isocitrate + NAD+ = 2-oxoglutarate + CO2 + NADH
chemical mechanism on the basis of the pH dependence of kinetic parameters, dissociation constants for competitive inhibitors, and multiple-substrate deuterium/13C isotope effects suggesting a stepwise mechanism with hydride transfer preceding decarboxylation, the decarboxylation step contributes only slightly to rate limitation, overview
Saccharomyces cerevisiae
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.1.1.87
2(R),3(S)-homoisocitrate + NAD+
with homoisocitrate as the substrate, no primary deuterium isotope effect is observed, and a small 13C kinetic isotope effect indicates that the decarboxylation step contributes only slightly to rate limitation
685232
Saccharomyces cerevisiae
alpha-ketoadipate + NADH + CO2 + H+
-
-
-
?
1.1.1.87
homoisocitrate + NAD+
-
685232
Saccharomyces cerevisiae
alpha-ketoadipate + NADH + CO2 + H+
-
-
-
r
1.1.1.87
isocitrate + NAD+
-
685232
Saccharomyces cerevisiae
?
-
-
-
r
1.1.1.87
threo-D-isocitric acid + NAD+
with isocitrate as the substrate, primary deuterium and 13C isotope effects indicate that hydride transfer and decarboxylation steps contribute to rate limitation, and that the decarboxylation step is the more rate-limiting of the two. The multiple-substrate deuterium/13C isotope effects suggest a stepwise mechanism with hydride transfer preceding decarboxylation
685232
Saccharomyces cerevisiae
?
-
-
-
?
1.1.1.286
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD+
chemical mechanism, stereochemistry of hydride transfer to NAD, overview
685232
Saccharomyces cerevisiae
2-oxoadipate + CO2 + NADH + H+
-
-
-
?
1.1.1.286
isocitrate + NAD+
rapid equilibrium random catalytic mechanism, stereochemistry of hydride transfer to NAD, overview
685232
Saccharomyces cerevisiae
2-oxoglutarate + CO2 + NADH
-
-
-
?
1.1.1.286
additional information
the enzyme catalyzes the fourth reaction of the alpha-aminoadipate pathway for lysine biosynthesis, the conversion of homoisocitrate to alpha-ketoadipate using NAD+ as an oxidizing agent
685232
Saccharomyces cerevisiae
?
-
-
-
-
Temperature Optimum [°C]
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
1.1.1.87
7
-
reductive carboxylation
Saccharomyces cerevisiae
1.1.1.87
7.5
-
oxidative decarboxylation
Saccharomyces cerevisiae
1.1.1.87
25
-
assay at
Saccharomyces cerevisiae
1.1.1.286
25
-
assay at
Saccharomyces cerevisiae
pH Optimum
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
1.1.1.87
7.5
-
assay at
Saccharomyces cerevisiae
1.1.1.286
8
-
assay at
Saccharomyces cerevisiae
pH Range
EC Number
pH Minimum
pH Maximum
Commentary
Organism
1.1.1.286
5
10
pH-profile, overview
Saccharomyces cerevisiae
pH Stability
EC Number
pH Stability
pH Stability Maximum
Commentary
Organism
1.1.1.87
additional information
-
enzyme is stable when incubated for at least 15 min over the pH range of 5.0-10.0
Saccharomyces cerevisiae
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.286
NAD+
stereochemistry of hydride transfer to NAD, overview
Saccharomyces cerevisiae
Ki Value [mM]
EC Number
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
1.1.1.87
0.002
-
Mg-homoisocitrate
oxidate decarboxylation of homoisocitrate
Saccharomyces cerevisiae
1.1.1.286
0.043
-
3-carboxypropylidenemalate
pH 8.0, 25°C, versus homoisocitrate
Saccharomyces cerevisiae
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.286
NAD+
stereochemistry of hydride transfer to NAD, overview
Saccharomyces cerevisiae
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
1.1.1.87
3-carboxypropylidenemalate
-
Saccharomyces cerevisiae
1.1.1.87
Mg-homoisocitrate
-
Saccharomyces cerevisiae
1.1.1.286
3-carboxypropylidenemalate
a dead-end inhibitor, competitive versus homoisocitrate
Saccharomyces cerevisiae
1.1.1.286
homoisocitrate
competitive, pH-dependent substrate inhibition
Saccharomyces cerevisiae
1.1.1.286
isocitrate
competitive, pH-dependent substrate inhibition
Saccharomyces cerevisiae
Ki Value [mM] (protein specific)
EC Number
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
1.1.1.87
0.002
-
Mg-homoisocitrate
oxidate decarboxylation of homoisocitrate
Saccharomyces cerevisiae
1.1.1.286
0.043
-
3-carboxypropylidenemalate
pH 8.0, 25°C, versus homoisocitrate
Saccharomyces cerevisiae
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
1.1.1.87
0.0042
-
Mg-homoisocitrate
oxidate decarboxylation of homoisocitrate
Saccharomyces cerevisiae
1.1.1.87
0.09
-
NADH
reductive carboxylation of alpha-ketoadipate
Saccharomyces cerevisiae
1.1.1.87
0.45
-
NAD+
oxidate decarboxylation of homoisocitrate
Saccharomyces cerevisiae
1.1.1.87
3.2
-
Mg-homoisocitrate
reductive carboxylation of alpha-ketoadipate
Saccharomyces cerevisiae
1.1.1.87
16.3
-
CO2
reductive carboxylation of alpha-ketoadipate
Saccharomyces cerevisiae
1.1.1.286
additional information
-
additional information
kinetic mechanism, detailed overview
Saccharomyces cerevisiae
Metals/Ions (protein specific)
EC Number
Metals/Ions
Commentary
Organism
Structure
1.1.1.87
Mg2+
-
Saccharomyces cerevisiae
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.1.1.286
additional information
Saccharomyces cerevisiae
the enzyme catalyzes the fourth reaction of the alpha-aminoadipate pathway for lysine biosynthesis, the conversion of homoisocitrate to alpha-ketoadipate using NAD+ as an oxidizing agent
?
-
-
-
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.1.1.87
2(R),3(S)-homoisocitrate + NAD+
with homoisocitrate as the substrate, no primary deuterium isotope effect is observed, and a small 13C kinetic isotope effect indicates that the decarboxylation step contributes only slightly to rate limitation
685232
Saccharomyces cerevisiae
alpha-ketoadipate + NADH + CO2 + H+
-
-
-
?
1.1.1.87
homoisocitrate + NAD+
-
685232
Saccharomyces cerevisiae
alpha-ketoadipate + NADH + CO2 + H+
-
-
-
r
1.1.1.87
isocitrate + NAD+
-
685232
Saccharomyces cerevisiae
?
-
-
-
r
1.1.1.87
threo-D-isocitric acid + NAD+
with isocitrate as the substrate, primary deuterium and 13C isotope effects indicate that hydride transfer and decarboxylation steps contribute to rate limitation, and that the decarboxylation step is the more rate-limiting of the two. The multiple-substrate deuterium/13C isotope effects suggest a stepwise mechanism with hydride transfer preceding decarboxylation
685232
Saccharomyces cerevisiae
?
-
-
-
?
1.1.1.286
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD+
chemical mechanism, stereochemistry of hydride transfer to NAD, overview
685232
Saccharomyces cerevisiae
2-oxoadipate + CO2 + NADH + H+
-
-
-
?
1.1.1.286
isocitrate + NAD+
rapid equilibrium random catalytic mechanism, stereochemistry of hydride transfer to NAD, overview
685232
Saccharomyces cerevisiae
2-oxoglutarate + CO2 + NADH
-
-
-
?
1.1.1.286
additional information
the enzyme catalyzes the fourth reaction of the alpha-aminoadipate pathway for lysine biosynthesis, the conversion of homoisocitrate to alpha-ketoadipate using NAD+ as an oxidizing agent
685232
Saccharomyces cerevisiae
?
-
-
-
-
Temperature Optimum [°C] (protein specific)
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
1.1.1.87
7
-
reductive carboxylation
Saccharomyces cerevisiae
1.1.1.87
7.5
-
oxidative decarboxylation
Saccharomyces cerevisiae
1.1.1.87
25
-
assay at
Saccharomyces cerevisiae
1.1.1.286
25
-
assay at
Saccharomyces cerevisiae
pH Optimum (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
1.1.1.87
7.5
-
assay at
Saccharomyces cerevisiae
1.1.1.286
8
-
assay at
Saccharomyces cerevisiae
pH Range (protein specific)
EC Number
pH Minimum
pH Maximum
Commentary
Organism
1.1.1.286
5
10
pH-profile, overview
Saccharomyces cerevisiae
pH Stability (protein specific)
EC Number
pH Stability
pH Stability Maximum
Commentary
Organism
1.1.1.87
additional information
-
enzyme is stable when incubated for at least 15 min over the pH range of 5.0-10.0
Saccharomyces cerevisiae