BRENDA - Enzyme Database

Crystal structure studies of NADP+ dependent isocitrate dehydrogenase from Thermus thermophilus exhibiting a novel terminal domain

Kumar, S.M.; Pampa, K.J.; Manjula, M.; Abdoh, M.M.; Kunishima, N.; Lokanath, N.K.; Biochem. Biophys. Res. Commun. 449, 107-113 (2014)

Data extracted from this reference:

Crystallization (Commentary)
EC Number
Crystallization
Organism
1.1.1.42
enzyme in ternary complex with citrate and cofactor NADP+, X-ray diffraction structure determination and analysis at 1.80 A resolution
Thermus thermophilus
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.1.1.42
isocitrate + NADP+
Thermus thermophilus
-
oxalosuccinate + NADPH + H+
-
-
r
1.1.1.42
oxalosuccinate
Thermus thermophilus
-
2-oxoglutarate + CO2
-
-
r
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
1.1.1.42
Thermus thermophilus
P33197
-
-
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.1.1.42
isocitrate + NADP+
-
739990
Thermus thermophilus
oxalosuccinate + NADPH + H+
-
-
-
r
1.1.1.42
additional information
the isocitrate molecule is located at the active site, and interacts with residues at the cleft between the large and small domain. The catalytic triad residues Lys191, Asp248 and Tyr144 are conserved and interact with isocitrate
739990
Thermus thermophilus
?
-
-
-
-
1.1.1.42
oxalosuccinate
-
739990
Thermus thermophilus
2-oxoglutarate + CO2
-
-
-
r
Subunits
EC Number
Subunits
Commentary
Organism
1.1.1.42
More
the overall fold of the enzyme protein is resolved into large domain, small domain and a clasp domain. The monomeric structure reveals also a unique terminal domain involved in dimerization. The overall TtIDH structure exhibits a closed conformation with the conserved catalytic triad residues Tyr144, Asp248, and Lys191. Oligomerization of the protein is determined using interface area and subunit–subunit interactions between protomers
Thermus thermophilus
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.42
NADP+
binding site structure
Thermus thermophilus
1.1.1.42
NADPH
-
Thermus thermophilus
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.42
NADP+
binding site structure
Thermus thermophilus
1.1.1.42
NADPH
-
Thermus thermophilus
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
1.1.1.42
enzyme in ternary complex with citrate and cofactor NADP+, X-ray diffraction structure determination and analysis at 1.80 A resolution
Thermus thermophilus
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.1.1.42
isocitrate + NADP+
Thermus thermophilus
-
oxalosuccinate + NADPH + H+
-
-
r
1.1.1.42
oxalosuccinate
Thermus thermophilus
-
2-oxoglutarate + CO2
-
-
r
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.1.1.42
isocitrate + NADP+
-
739990
Thermus thermophilus
oxalosuccinate + NADPH + H+
-
-
-
r
1.1.1.42
additional information
the isocitrate molecule is located at the active site, and interacts with residues at the cleft between the large and small domain. The catalytic triad residues Lys191, Asp248 and Tyr144 are conserved and interact with isocitrate
739990
Thermus thermophilus
?
-
-
-
-
1.1.1.42
oxalosuccinate
-
739990
Thermus thermophilus
2-oxoglutarate + CO2
-
-
-
r
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
1.1.1.42
More
the overall fold of the enzyme protein is resolved into large domain, small domain and a clasp domain. The monomeric structure reveals also a unique terminal domain involved in dimerization. The overall TtIDH structure exhibits a closed conformation with the conserved catalytic triad residues Tyr144, Asp248, and Lys191. Oligomerization of the protein is determined using interface area and subunit–subunit interactions between protomers
Thermus thermophilus
General Information
EC Number
General Information
Commentary
Organism
1.1.1.42
evolution
the overall fold of the enzyme protein is resolved into large domain, small domain and a clasp domain. The monomeric structure reveals also a terminal domain involved in dimerization, a very unique domain when compared to other IDHs. The small domain and clasp domain show significant differences when compared to other IDHs of the same subfamily. The structure of TtIDH reveals the absence of helix at the clasp domain, which is mainly involved in oligomerization in other IDHs. Also, helices/beta sheets are absent in the small domain, when compared to other IDHs of the same subfamily. The overall TtIDH structure exhibits a closed conformation with the conserved catalytic triad residues Tyr144, Asp248, and Lys191. Oligomerization of the protein is determined using interface area and subunit–subunit interactions between protomers. The TtIDH structure with the terminal domain may be categorized as a first structure of a type IV subfamily
Thermus thermophilus
General Information (protein specific)
EC Number
General Information
Commentary
Organism
1.1.1.42
evolution
the overall fold of the enzyme protein is resolved into large domain, small domain and a clasp domain. The monomeric structure reveals also a terminal domain involved in dimerization, a very unique domain when compared to other IDHs. The small domain and clasp domain show significant differences when compared to other IDHs of the same subfamily. The structure of TtIDH reveals the absence of helix at the clasp domain, which is mainly involved in oligomerization in other IDHs. Also, helices/beta sheets are absent in the small domain, when compared to other IDHs of the same subfamily. The overall TtIDH structure exhibits a closed conformation with the conserved catalytic triad residues Tyr144, Asp248, and Lys191. Oligomerization of the protein is determined using interface area and subunit–subunit interactions between protomers. The TtIDH structure with the terminal domain may be categorized as a first structure of a type IV subfamily
Thermus thermophilus