Crystal Structure Of The Monomeric Isocitrate Dehydrogenase In Complex With NADP+

Experimental Data Snapshot

  • Resolution: 3.20 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.260 

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Crystal Structure of the Monomeric Isocitrate Dehydrogenase in the Presence of NADP+

Yasutake, Y.Watanabe, S.Yao, M.Takada, Y.Fukunaga, N.Tanaka, I.

(2003) J Biol Chem 278: 36897-36904

  • DOI: https://doi.org/10.1074/jbc.M304091200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    NADP+-dependent monomeric isocitrate dehydrogenase (IDH) from the nitrogen-fixing bacterium Azotobacter vinelandii (AvIDH) is one of members of the beta-decarboxylating dehydrogenase family and catalyzes the dehydration and decarboxylation of isocitrate to yield 2-oxoglutrate and CO2 in the Krebs cycle. We solved the crystal structure of the AvIDH in complex with cofactor NADP+ (AvIDH-NADP+ complex). The final refined model shows the closed form that has never been detected in any previously solved structures of beta-decarboxylating dehydrogenases. The structure also reveals all of the residues that interact with NADP+. The structure-based sequence alignment reveals that these residues were not conserved in any other dimeric NADP+-dependent IDHs. Therefore the NADP+ specificity of the monomeric and dimeric IDHs was independently acquired through the evolutional process. The AvIDH was known to show an exceptionally high turnover rate. The structure of the AvIDH-NADP+ complex indicates that one loop, which is not present in the Escherichia coli IDHs, reliably stabilizes the conformation of the nicotinamide mononucleotide of the bound NADP+ by forming a few hydrogen bonds, and such interactions are considered to be important for the monomeric enzyme to initiate the hydride transfer reaction immediately. Finally, the structure of the AvIDH is compared with that of other dimeric NADP-IDHs. Several structural features demonstrate that the monomeric IDHs are structurally more related to the eukaryotic dimeric IDHs than to the bacterial dimeric IDHs.

  • Organizational Affiliation

    Division of Biological Sciences, Graduate School of Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isocitrate Dehydrogenase
A, B, C, D
741Azotobacter vinelandiiMutation(s): 0 
Find proteins for P16100 (Azotobacter vinelandii)
Explore P16100 
Go to UniProtKB:  P16100
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16100
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 3.20 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.260 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.496α = 90
b = 110.407β = 90.156
c = 133.698γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description