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

Structure. 1998 Aug 15;6(8):971-82. doi: 10.1016/s0969-2126(98)00099-9.


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 A 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 gamma-isopropyl group. The gamma 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 gamma-isopropyl moiety of IPM. A glutamic acid in domain 1, Glu88, participates in the formation of the hydrophobic pocket. The C beta and C gamma atoms of Glu88 interact with the gamma-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.

MeSH terms

  • 3-Isopropylmalate Dehydrogenase
  • Alcohol Oxidoreductases / chemistry*
  • Amino Acid Sequence
  • Bacterial Proteins / chemistry
  • Binding Sites / physiology
  • Crystallography, X-Ray
  • Malates / chemistry
  • Models, Molecular
  • Molecular Sequence Data
  • NAD / chemistry
  • Oxidoreductases / chemistry
  • Protein Conformation
  • Protein Folding
  • Protein Structure, Secondary
  • Sequence Alignment
  • Substrate Specificity
  • Thiobacillus / enzymology*


  • Bacterial Proteins
  • Malates
  • NAD
  • beta-isopropylmalate
  • Oxidoreductases
  • Alcohol Oxidoreductases
  • 3-Isopropylmalate Dehydrogenase

Associated data

  • PDB/1A05