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Literature summary for 1.1.1.286 extracted from

  • Takahashi, K.; Tomita, T.; Kuzuyama, T.; Nishiyama, M.
    Determinants of dual substrate specificity revealed by the crystal structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex with homoisocitrate-Mg(2+)-NADH (2016), Biochem. Biophys. Res. Commun., 478, 1688-1693.
    View publication on PubMed

Cloned(Commentary)

Cloned (Comment) Organism
recombinant expression in Escherichia coli strain Escherichia coli BL21(DE3)CodonPlus-RIL Thermus thermophilus

Crystallization (Commentary)

Crystallization (Comment) 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 Comment Organism Structure
(2S,3S)-thiahomoisocitrate
-
Thermus thermophilus

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment 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 Comment Organism Structure
Mg2+ binding strutcure analysis Thermus thermophilus

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
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 + H+
-
r
isocitrate + NAD+ Thermus thermophilus DSM 7039
-
2-oxoglutarate + CO2 + NADH + H+
-
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 UniProt Comment Textmining
Thermus thermophilus Q72IW9
-
-
Thermus thermophilus DSM 7039 Q72IW9
-
-

Purification (Commentary)

Purification (Comment) 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 Comment Substrates Organism Products Comment (Products) Rev. Reac.
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 + H+
-
r
isocitrate + NAD+
-
Thermus thermophilus DSM 7039 2-oxoglutarate + CO2 + NADH + H+
-
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 Thermus thermophilus ?
-
?
additional information dual substrate specificity for homoisocitrate dehydrogenase 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 Thermus thermophilus DSM 7039 ?
-
?
additional information dual substrate specificity for homoisocitrate dehydrogenase Thermus thermophilus DSM 7039 ?
-
?

Subunits

Subunits Comment Organism
tetramer dimer of dimers Thermus thermophilus

Synonyms

Synonyms Comment Organism
HICDH
-
Thermus thermophilus

Temperature Optimum [┬░C]

Temperature Optimum [┬░C] Temperature Optimum Maximum [┬░C] Comment Organism
60
-
assay at Thermus thermophilus

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment 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 Comment Organism
8
-
assay at Thermus thermophilus

Cofactor

Cofactor Comment 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

General Information

General Information Comment 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 Comment 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