Structure and quantum chemical analysis of NAD+-dependent isocitrate dehydrogenase: Hydride transfer and co-factor specificity

Katsumi Imada, Takashi Tamura, Ryo Takenaka, Issei Kobayashi, Keiichi Namba, Kenji Inagaki

Research output: Contribution to journalArticlepeer-review

19 Citations (Scopus)

Abstract

The crystal structure of Acidithiobacillus thiooxidans isocitrate dehydrogenase complexed with NAD+ and citrate has been solved to a resolution of 1.9 Å. The protein fold of this NAD+-dependent enzyme shares a high similarity with those of NADP+-dependent bacterial ICDHs. The NAD+ and the citrate are clearly identified in the active site cleft with a well-defined electron density. Asp-357 is the direct cofactor-specificity determinant that interacts with 2′-OH and 3′-OH of the adenosine ribose. The adenosine ribose takes a C2′-endo puckering conformation as previously reported for an NAD+-specific isopropylmalate dehydrogenase. The nicotinamide moiety of NAD+ has the amide NH2 group oriented in cis conformation with respect to the C4 carbon of the nicotinamide ring, slanted toward the bound citrate molecule with a dihedral angle of -21°. The semi-empirical molecular orbital calculation suggests that the pro-R hydrogen atom at C4 of NADH would bear the largest negative charge when the amide NH2 group is in such conformation, suggesting that the amide group has a catalytically significant role in stabilizing the transition state as NADH is being formed during the hydride transfer catalysis.

Original languageEnglish
Pages (from-to)63-71
Number of pages9
JournalProteins: Structure, Function and Genetics
Volume70
Issue number1
DOIs
Publication statusPublished - Jan 1 2008

Keywords

  • Chemolithotrophic bacterium
  • Crystal structure
  • Decarboxylating dehydrogenase
  • Hydride migration
  • Semi-empirical molecular orbital calculation

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

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