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

被引:66
作者
Imada, K
Inagaki, K
Matsunami, H
Kawaguchi, H
Tanaka, H
Tanaka, N
Namba, K
机构
[1] Matsushita Elect Ind Co Ltd, Int Inst Adv Res, Seika 61902, Japan
[2] Okayama Univ, Dept Bioresources Chem, Okayama 700, Japan
[3] Tokyo Inst Technol, Fac Biosci & Biotechnol, Midori Ku, Yokohama, Kanagawa 226, Japan
关键词
conformational change; 3-isopropylmalate dehydrogenase; substrate binding; X-ray crystallography;
D O I
10.1016/S0969-2126(98)00099-9
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Background: 3-Isopropylmalate dehydrogenase (IPMDH) and isocitrate dehydrogenase ([CDH) 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 Angstrom 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.
引用
收藏
页码:971 / 982
页数:12
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