BRENDA - Enzyme Database
show all sequences of 1.1.1.286

Determinants of dual substrate specificity revealed by the crystal structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex with homoisocitrate-Mg(2+)-NADH

Takahashi, K.; Tomita, T.; Kuzuyama, T.; Nishiyama, M.; Biochem. Biophys. Res. Commun. 478, 1688-1693 (2016)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
recombinant expression in Escherichia coli strain Escherichia coli BL21(DE3)CodonPlus-RIL
Thermus thermophilus
Crystallization (Commentary)
Crystallization
Organism
purified enzyme TtHICDH in quaternary complex with homoisocitrate, NADH, and Mg2+, X-ray diffraction strczure determination and analysis at 2.5 A resolution, molecular replacement using the apoform of TtHICDH, PDB ID 1X0L, at a resolution of 2.5 A
Thermus thermophilus
Inhibitors
Inhibitors
Commentary
Organism
Structure
(2S,3S)-thiahomoisocitrate
-
Thermus thermophilus
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.21
-
homoisocitrate
pH 8.0, 60°C, recombinant enzyme
Thermus thermophilus
0.29
-
isocitrate
pH 8.0, 60°C, recombinant enzyme
Thermus thermophilus
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Mg2+
binding strutcure analysis
Thermus thermophilus
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
homoisocitrate + NAD+
Thermus thermophilus
-
2-oxoadipate + CO2 + NADH + H+
-
-
r
homoisocitrate + NAD+
Thermus thermophilus DSM 7039
-
2-oxoadipate + CO2 + NADH + H+
-
-
r
isocitrate + NAD+
Thermus thermophilus
-
2-oxoglutarate + CO2 + NADH
-
-
r
isocitrate + NAD+
Thermus thermophilus DSM 7039
-
2-oxoglutarate + CO2 + NADH
-
-
r
additional information
Thermus thermophilus
in contrast to other homoisicitrate dehydrogenases, the homoisocitrate dehydrogenase from the thermophilic bacterium Thermus thermophilus (TtHICDH) catalyzes the reactions using both homoisocitrate and isocitrate as substrates at similar efficiencies
?
-
-
-
additional information
Thermus thermophilus DSM 7039
in contrast to other homoisicitrate dehydrogenases, the homoisocitrate dehydrogenase from the thermophilic bacterium Thermus thermophilus (TtHICDH) catalyzes the reactions using both homoisocitrate and isocitrate as substrates at similar efficiencies
?
-
-
-
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Thermus thermophilus
Q72IW9
-
-
Thermus thermophilus DSM 7039
Q72IW9
-
-
Purification (Commentary)
Commentary
Organism
recombinant enzyme from Escherichia coli by anion exchange chromatography, ammonium sufate fractionation, hydrophobic interaction chromatography, and gel filtration
Thermus thermophilus
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
homoisocitrate + NAD+
-
740000
Thermus thermophilus
2-oxoadipate + CO2 + NADH + H+
-
-
-
r
homoisocitrate + NAD+
-
740000
Thermus thermophilus DSM 7039
2-oxoadipate + CO2 + NADH + H+
-
-
-
r
isocitrate + NAD+
-
740000
Thermus thermophilus
2-oxoglutarate + CO2 + NADH
-
-
-
r
isocitrate + NAD+
-
740000
Thermus thermophilus DSM 7039
2-oxoglutarate + CO2 + NADH
-
-
-
r
additional information
in contrast to other homoisicitrate dehydrogenases, the homoisocitrate dehydrogenase from the thermophilic bacterium Thermus thermophilus (TtHICDH) catalyzes the reactions using both homoisocitrate and isocitrate as substrates at similar efficiencies
740000
Thermus thermophilus
?
-
-
-
-
additional information
dual substrate specificity for homoisocitrate dehydrogenase
740000
Thermus thermophilus
?
-
-
-
-
additional information
in contrast to other homoisicitrate dehydrogenases, the homoisocitrate dehydrogenase from the thermophilic bacterium Thermus thermophilus (TtHICDH) catalyzes the reactions using both homoisocitrate and isocitrate as substrates at similar efficiencies
740000
Thermus thermophilus DSM 7039
?
-
-
-
-
additional information
dual substrate specificity for homoisocitrate dehydrogenase
740000
Thermus thermophilus DSM 7039
?
-
-
-
-
Subunits
Subunits
Commentary
Organism
tetramer
dimer of dimers
Thermus thermophilus
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
60
-
assay at
Thermus thermophilus
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
33
-
homoisocitrate
pH 8.0, 60°C, recombinant enzyme
Thermus thermophilus
76
-
isocitrate
pH 8.0, 60°C, recombinant enzyme
Thermus thermophilus
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
8
-
assay at
Thermus thermophilus
Cofactor
Cofactor
Commentary
Organism
Structure
NAD+
-
Thermus thermophilus
NADH
NADH forms specific contacts with enzyme TtHICDH. The 2'- and 3-OHs of the adenine ribose of NADH form hydrogen bonds with Asp265 conserved among HICDHs, which may serve as a determinant for the preference of HICDH family members for NAD+ to NADP+
Thermus thermophilus
Cloned(Commentary) (protein specific)
Commentary
Organism
recombinant expression in Escherichia coli strain Escherichia coli BL21(DE3)CodonPlus-RIL
Thermus thermophilus
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
NAD+
-
Thermus thermophilus
NADH
NADH forms specific contacts with enzyme TtHICDH. The 2'- and 3-OHs of the adenine ribose of NADH form hydrogen bonds with Asp265 conserved among HICDHs, which may serve as a determinant for the preference of HICDH family members for NAD+ to NADP+
Thermus thermophilus
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified enzyme TtHICDH in quaternary complex with homoisocitrate, NADH, and Mg2+, X-ray diffraction strczure determination and analysis at 2.5 A resolution, molecular replacement using the apoform of TtHICDH, PDB ID 1X0L, at a resolution of 2.5 A
Thermus thermophilus
Inhibitors (protein specific)
Inhibitors
Commentary
Organism
Structure
(2S,3S)-thiahomoisocitrate
-
Thermus thermophilus
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.21
-
homoisocitrate
pH 8.0, 60°C, recombinant enzyme
Thermus thermophilus
0.29
-
isocitrate
pH 8.0, 60°C, recombinant enzyme
Thermus thermophilus
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Mg2+
binding strutcure analysis
Thermus thermophilus
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
homoisocitrate + NAD+
Thermus thermophilus
-
2-oxoadipate + CO2 + NADH + H+
-
-
r
homoisocitrate + NAD+
Thermus thermophilus DSM 7039
-
2-oxoadipate + CO2 + NADH + H+
-
-
r
isocitrate + NAD+
Thermus thermophilus
-
2-oxoglutarate + CO2 + NADH
-
-
r
isocitrate + NAD+
Thermus thermophilus DSM 7039
-
2-oxoglutarate + CO2 + NADH
-
-
r
additional information
Thermus thermophilus
in contrast to other homoisicitrate dehydrogenases, the homoisocitrate dehydrogenase from the thermophilic bacterium Thermus thermophilus (TtHICDH) catalyzes the reactions using both homoisocitrate and isocitrate as substrates at similar efficiencies
?
-
-
-
additional information
Thermus thermophilus DSM 7039
in contrast to other homoisicitrate dehydrogenases, the homoisocitrate dehydrogenase from the thermophilic bacterium Thermus thermophilus (TtHICDH) catalyzes the reactions using both homoisocitrate and isocitrate as substrates at similar efficiencies
?
-
-
-
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant enzyme from Escherichia coli by anion exchange chromatography, ammonium sufate fractionation, hydrophobic interaction chromatography, and gel filtration
Thermus thermophilus
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
homoisocitrate + NAD+
-
740000
Thermus thermophilus
2-oxoadipate + CO2 + NADH + H+
-
-
-
r
homoisocitrate + NAD+
-
740000
Thermus thermophilus DSM 7039
2-oxoadipate + CO2 + NADH + H+
-
-
-
r
isocitrate + NAD+
-
740000
Thermus thermophilus
2-oxoglutarate + CO2 + NADH
-
-
-
r
isocitrate + NAD+
-
740000
Thermus thermophilus DSM 7039
2-oxoglutarate + CO2 + NADH
-
-
-
r
additional information
in contrast to other homoisicitrate dehydrogenases, the homoisocitrate dehydrogenase from the thermophilic bacterium Thermus thermophilus (TtHICDH) catalyzes the reactions using both homoisocitrate and isocitrate as substrates at similar efficiencies
740000
Thermus thermophilus
?
-
-
-
-
additional information
dual substrate specificity for homoisocitrate dehydrogenase
740000
Thermus thermophilus
?
-
-
-
-
additional information
in contrast to other homoisicitrate dehydrogenases, the homoisocitrate dehydrogenase from the thermophilic bacterium Thermus thermophilus (TtHICDH) catalyzes the reactions using both homoisocitrate and isocitrate as substrates at similar efficiencies
740000
Thermus thermophilus DSM 7039
?
-
-
-
-
additional information
dual substrate specificity for homoisocitrate dehydrogenase
740000
Thermus thermophilus DSM 7039
?
-
-
-
-
Subunits (protein specific)
Subunits
Commentary
Organism
tetramer
dimer of dimers
Thermus thermophilus
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
60
-
assay at
Thermus thermophilus
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
33
-
homoisocitrate
pH 8.0, 60°C, recombinant enzyme
Thermus thermophilus
76
-
isocitrate
pH 8.0, 60°C, recombinant enzyme
Thermus thermophilus
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
8
-
assay at
Thermus thermophilus
General Information
General Information
Commentary
Organism
evolution
homoisocitrate dehydrogenase, HICDH, is a member of the beta-decarboxylating dehydrogenase family
Thermus thermophilus
metabolism
in contrast to other homoisocitrate dehydrogenases, the enzyme from the thermophilic bacterium Thermus thermophilus (TtHICDH) catalyzes the reactions using both homoisocitrate and isocitrate as substrates at similar efficiencies. The enzyme catalyzes the conversion of homoisocitrate to 2-oxoadipate using NAD+ as a coenzyme, which is the fourth reaction involved in lysine biosynthesis through the alpha-aminoadipate pathway
Thermus thermophilus
additional information
enzyme structure modelling and molecular dynamics, the distal carboxyl group of homoiscitrate is recognized by the side chains of Ser72 and Arg85 from one subunit, and Asn173 from another subunit of a dimer unit. The enzyme recognizes the distal carboxyl group of isocitrate by Arg85 in the model. Active site structure analysis, the active site is located in the cleft between two domains. In the quaternary complex of TtHICDH, the basic residues, Arg88, Arg96, Arg118, Tyr125, and Lys171, recognize the malate moiety of HIC. Asp204 (from the otherdimer part) , Asp228, Asp232, and water molecules bind a Mg2+ ion in an octahedral coordination manner similar to those of other substrate-bound structures, e.g. PDB ID 4F7I
Thermus thermophilus
General Information (protein specific)
General Information
Commentary
Organism
evolution
homoisocitrate dehydrogenase, HICDH, is a member of the beta-decarboxylating dehydrogenase family
Thermus thermophilus
metabolism
in contrast to other homoisocitrate dehydrogenases, the enzyme from the thermophilic bacterium Thermus thermophilus (TtHICDH) catalyzes the reactions using both homoisocitrate and isocitrate as substrates at similar efficiencies. The enzyme catalyzes the conversion of homoisocitrate to 2-oxoadipate using NAD+ as a coenzyme, which is the fourth reaction involved in lysine biosynthesis through the alpha-aminoadipate pathway
Thermus thermophilus
additional information
enzyme structure modelling and molecular dynamics, the distal carboxyl group of homoiscitrate is recognized by the side chains of Ser72 and Arg85 from one subunit, and Asn173 from another subunit of a dimer unit. The enzyme recognizes the distal carboxyl group of isocitrate by Arg85 in the model. Active site structure analysis, the active site is located in the cleft between two domains. In the quaternary complex of TtHICDH, the basic residues, Arg88, Arg96, Arg118, Tyr125, and Lys171, recognize the malate moiety of HIC. Asp204 (from the otherdimer part) , Asp228, Asp232, and water molecules bind a Mg2+ ion in an octahedral coordination manner similar to those of other substrate-bound structures, e.g. PDB ID 4F7I
Thermus thermophilus
KCat/KM [mM/s]
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
157.1
-
homoisocitrate
pH 8.0, 60°C, recombinant enzyme
Thermus thermophilus
262.1
-
isocitrate
pH 8.0, 60°C, recombinant enzyme
Thermus thermophilus
KCat/KM [mM/s] (protein specific)
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
157.1
-
homoisocitrate
pH 8.0, 60°C, recombinant enzyme
Thermus thermophilus
262.1
-
isocitrate
pH 8.0, 60°C, recombinant enzyme
Thermus thermophilus
Other publictions for EC 1.1.1.286
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
740021
Shimizu
Structure and function of an a ...
Thermococcus kodakarensis, Thermococcus kodakarensis KRD1
Biochem. J.
474
105-122
2017
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-
1
1
6
-
-
32
-
1
-
4
-
5
-
-
1
-
-
-
-
-
8
1
1
-
-
16
1
-
-
1
-
-
-
-
-
1
1
1
6
-
-
-
-
32
-
1
-
4
-
-
-
1
-
-
-
-
8
1
1
-
-
16
1
-
-
-
-
3
3
-
31
31
738195
Takahashi
Characterization of two ?-deca ...
Sulfolobus acidocaldarius, Sulfolobus acidocaldarius MW001
Extremophiles
20
843-853
2016
-
-
1
-
-
-
-
2
-
-
-
6
-
5
-
-
1
-
-
-
-
-
6
1
1
-
-
2
1
-
-
2
-
-
-
-
-
1
2
-
-
-
-
-
-
2
-
-
-
6
-
-
-
1
-
-
-
-
6
1
1
-
-
2
1
-
-
-
-
1
1
-
2
2
740000
Takahashi
Determinants of dual substrate ...
Thermus thermophilus, Thermus thermophilus DSM 7039
Biochem. Biophys. Res. Commun.
478
1688-1693
2016
-
-
1
1
-
-
1
2
-
1
-
6
-
2
-
-
1
-
-
-
-
-
8
1
1
-
-
2
1
-
-
2
-
-
-
-
-
1
2
1
-
-
-
1
-
2
-
1
-
6
-
-
-
1
-
-
-
-
8
1
1
-
-
2
1
-
-
-
-
3
3
-
2
2
685232
Lin
Chemical mechanism of homoisoc ...
Saccharomyces cerevisiae
Biochemistry
47
4169-4180
2008
-
-
-
-
-
-
3
1
-
-
-
1
-
1
-
-
-
2
-
-
-
-
3
-
1
-
-
-
1
1
-
1
1
-
-
-
-
-
1
-
-
-
-
3
1
1
-
-
-
1
-
-
-
-
-
-
-
-
3
-
1
-
-
-
1
1
-
-
-
-
-
-
-
-
696220
Lin
Potassium is an activator of h ...
Saccharomyces cerevisiae
Biochemistry
47
10809-10815
2008
-
-
-
-
-
-
4
-
-
4
-
1
-
1
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
1
3
-
-
-
-
-
1
-
-
-
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4
3
-
-
4
-
1
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
660907
Miyazaki
Bifunctional isocitrate-homois ...
Pyrococcus horikoshii
Biochem. Biophys. Res. Commun.
331
341-346
2005
-
-
1
-
-
-
-
3
-
-
-
-
-
3
-
-
1
-
-
-
-
-
4
-
-
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3
-
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1
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3
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1
-
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-
-
4
-
-
-
-
3
-
-
-
-
-
-
-
-
-
-
660918
Miyazaki
Identification of a novel trif ...
Deinococcus radiodurans
Biochem. Biophys. Res. Commun.
336
596-602
2005
-
-
-
-
4
-
3
8
-
3
3
-
-
1
-
-
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-
-
-
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5
1
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8
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1
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1
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4
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3
-
8
-
3
3
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5
1
-
-
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8
-
-
-
-
-
-
-
-
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-
656127
Miyazaki
Characterization of homoisocit ...
Thermus thermophilus, Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039
J. Biol. Chem.
278
1864-1871
2003
-
-
1
-
1
-
-
2
-
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2
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-
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6
1
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1
2
-
-
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-
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1
-
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1
-
-
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2
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6
1
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1
2
-
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-
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-
-