Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 Å resolution: The role of Glu88 in the unique substrate-recognition mechanism

Katsumi Imada, Kenji Inagaki, Hideyuki Matsunami, Hiroshi Kawaguchi, Hidehiko Tanaka, Nobuo Tanaka, Keiichi Namba

Research output: Contribution to journalArticle

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Abstract

Background: 3-Isopropylmalate dehydrogenase (IPMDH) and isocitrate dehydrogenase (ICDH) belong to a unique family of bifunctional decarboxylating dehydrogenases. Although the ICDH dimer catalyzes its reaction under a closed conformation, known structures of the IPMDH dimer (without substrate) adopt a fully open or a partially closed form. Considering the similarity in the catalytic mechanism, the IPMDH dimer must be in a fully closed conformation during the reaction. A large conformational change should therefore occur upon substrate binding. Results: We have determined the crystal structure of IPMDH from Thiobacillus ferrooxidans (Tf) complexed with 3-isopropylmalate (IPM) at 2.0 Å resolution by the molecular replacement method. The structure shows a fully closed conformation and the substrate-binding site is quite similar to that of ICDH except for a region around the γ-isopropyl group. The γ group is recognized by a unique hydrophobic pocket, which includes Glu88, Leu91 and Leu92 from subunit 1 and Val193' from subunit 2. Conclusions: A large movement of domain 1 is induced by substrate binding, which results in the formation of the hydrophobic pocket for the γ-isopropyl moiety of IPM. A glutamic acid in domain 1, Glu88, participates in the formation of the hydrophobic pocket. The Cβ and Cγ atoms of Glu88 interact with the γ-isopropyl moiety of IPM and are central to the recognition of substrate. The acidic tip of Glu88 is likely to interact with the nicotinamide mononucleotide (NMN) ribose of NAD+ in the ternary complex. This structure clearly explains the substrate specificity of IPMDH.

Original languageEnglish
Pages (from-to)971-982
Number of pages12
JournalStructure
Volume6
Issue number8
Publication statusPublished - Aug 15 1998

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3-Isopropylmalate Dehydrogenase
Oxidoreductases
Isocitrate Dehydrogenase
Nicotinamide Mononucleotide
Thiobacillus
Substrate Specificity
NAD
Glutamic Acid
Binding Sites
beta-isopropylmalate

Keywords

  • 3-isopropylmalate dehydrogenase
  • Conformational change
  • Substrate binding
  • X-ray crystallography

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology

Cite this

Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 Å resolution : The role of Glu88 in the unique substrate-recognition mechanism. / Imada, Katsumi; Inagaki, Kenji; Matsunami, Hideyuki; Kawaguchi, Hiroshi; Tanaka, Hidehiko; Tanaka, Nobuo; Namba, Keiichi.

In: Structure, Vol. 6, No. 8, 15.08.1998, p. 971-982.

Research output: Contribution to journalArticle

Imada, Katsumi ; Inagaki, Kenji ; Matsunami, Hideyuki ; Kawaguchi, Hiroshi ; Tanaka, Hidehiko ; Tanaka, Nobuo ; Namba, Keiichi. / Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 Å resolution : The role of Glu88 in the unique substrate-recognition mechanism. In: Structure. 1998 ; Vol. 6, No. 8. pp. 971-982.
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abstract = "Background: 3-Isopropylmalate dehydrogenase (IPMDH) and isocitrate dehydrogenase (ICDH) belong to a unique family of bifunctional decarboxylating dehydrogenases. Although the ICDH dimer catalyzes its reaction under a closed conformation, known structures of the IPMDH dimer (without substrate) adopt a fully open or a partially closed form. Considering the similarity in the catalytic mechanism, the IPMDH dimer must be in a fully closed conformation during the reaction. A large conformational change should therefore occur upon substrate binding. Results: We have determined the crystal structure of IPMDH from Thiobacillus ferrooxidans (Tf) complexed with 3-isopropylmalate (IPM) at 2.0 {\AA} resolution by the molecular replacement method. The structure shows a fully closed conformation and the substrate-binding site is quite similar to that of ICDH except for a region around the γ-isopropyl group. The γ group is recognized by a unique hydrophobic pocket, which includes Glu88, Leu91 and Leu92 from subunit 1 and Val193' from subunit 2. Conclusions: A large movement of domain 1 is induced by substrate binding, which results in the formation of the hydrophobic pocket for the γ-isopropyl moiety of IPM. A glutamic acid in domain 1, Glu88, participates in the formation of the hydrophobic pocket. The Cβ and Cγ atoms of Glu88 interact with the γ-isopropyl moiety of IPM and are central to the recognition of substrate. The acidic tip of Glu88 is likely to interact with the nicotinamide mononucleotide (NMN) ribose of NAD+ in the ternary complex. This structure clearly explains the substrate specificity of IPMDH.",
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AU - Inagaki, Kenji

AU - Matsunami, Hideyuki

AU - Kawaguchi, Hiroshi

AU - Tanaka, Hidehiko

AU - Tanaka, Nobuo

AU - Namba, Keiichi

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N2 - Background: 3-Isopropylmalate dehydrogenase (IPMDH) and isocitrate dehydrogenase (ICDH) belong to a unique family of bifunctional decarboxylating dehydrogenases. Although the ICDH dimer catalyzes its reaction under a closed conformation, known structures of the IPMDH dimer (without substrate) adopt a fully open or a partially closed form. Considering the similarity in the catalytic mechanism, the IPMDH dimer must be in a fully closed conformation during the reaction. A large conformational change should therefore occur upon substrate binding. Results: We have determined the crystal structure of IPMDH from Thiobacillus ferrooxidans (Tf) complexed with 3-isopropylmalate (IPM) at 2.0 Å resolution by the molecular replacement method. The structure shows a fully closed conformation and the substrate-binding site is quite similar to that of ICDH except for a region around the γ-isopropyl group. The γ group is recognized by a unique hydrophobic pocket, which includes Glu88, Leu91 and Leu92 from subunit 1 and Val193' from subunit 2. Conclusions: A large movement of domain 1 is induced by substrate binding, which results in the formation of the hydrophobic pocket for the γ-isopropyl moiety of IPM. A glutamic acid in domain 1, Glu88, participates in the formation of the hydrophobic pocket. The Cβ and Cγ atoms of Glu88 interact with the γ-isopropyl moiety of IPM and are central to the recognition of substrate. The acidic tip of Glu88 is likely to interact with the nicotinamide mononucleotide (NMN) ribose of NAD+ in the ternary complex. This structure clearly explains the substrate specificity of IPMDH.

AB - Background: 3-Isopropylmalate dehydrogenase (IPMDH) and isocitrate dehydrogenase (ICDH) belong to a unique family of bifunctional decarboxylating dehydrogenases. Although the ICDH dimer catalyzes its reaction under a closed conformation, known structures of the IPMDH dimer (without substrate) adopt a fully open or a partially closed form. Considering the similarity in the catalytic mechanism, the IPMDH dimer must be in a fully closed conformation during the reaction. A large conformational change should therefore occur upon substrate binding. Results: We have determined the crystal structure of IPMDH from Thiobacillus ferrooxidans (Tf) complexed with 3-isopropylmalate (IPM) at 2.0 Å resolution by the molecular replacement method. The structure shows a fully closed conformation and the substrate-binding site is quite similar to that of ICDH except for a region around the γ-isopropyl group. The γ group is recognized by a unique hydrophobic pocket, which includes Glu88, Leu91 and Leu92 from subunit 1 and Val193' from subunit 2. Conclusions: A large movement of domain 1 is induced by substrate binding, which results in the formation of the hydrophobic pocket for the γ-isopropyl moiety of IPM. A glutamic acid in domain 1, Glu88, participates in the formation of the hydrophobic pocket. The Cβ and Cγ atoms of Glu88 interact with the γ-isopropyl moiety of IPM and are central to the recognition of substrate. The acidic tip of Glu88 is likely to interact with the nicotinamide mononucleotide (NMN) ribose of NAD+ in the ternary complex. This structure clearly explains the substrate specificity of IPMDH.

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