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 journalArticle

16 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 2008

Fingerprint

Transfer Factor
Isocitrate Dehydrogenase
Hydrides
NAD
Chemical analysis
Amides
Citric Acid
Conformations
Ribose
Niacinamide
Adenosine
Acidithiobacillus thiooxidans
Orbital calculations
Molecular orbitals
Dihedral angle
Catalysis
NADP
Carrier concentration
Hydrogen
Catalytic Domain

Keywords

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

ASJC Scopus subject areas

  • Genetics
  • Structural Biology
  • Biochemistry

Cite this

Structure and quantum chemical analysis of NAD+-dependent isocitrate dehydrogenase : Hydride transfer and co-factor specificity. / Imada, Katsumi; Tamura, Takashi; Takenaka, Ryo; Kobayashi, Issei; Namba, Keiichi; Inagaki, Kenji.

In: Proteins: Structure, Function and Genetics, Vol. 70, No. 1, 01.2008, p. 63-71.

Research output: Contribution to journalArticle

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