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

64 Citations (Scopus)


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
Issue number8
Publication statusPublished - Aug 15 1998



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

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

Cite this