Crystal structure of the monomeric isocitrate dehydrogenase in complex with isocitrate and Mn

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Structure of the Monomeric Isocitrate Dehydrogenase: Evidence of a Protein Monomerization by a Domain Duplication

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

(2002) Structure 10: 1637-1648

  • DOI: https://doi.org/10.1016/s0969-2126(02)00904-8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    NADP(+)-dependent isocitrate dehydrogenase is a member of the beta-decarboxylating dehydrogenase family and catalyzes the oxidative decarboxylation reaction from 2R,3S-isocitrate to yield 2-oxoglutarate and CO(2) in the Krebs cycle. Although most prokaryotic NADP(+)-dependent isocitrate dehydrogenases (IDHs) are homodimeric enzymes, the monomeric IDH with a molecular weight of 80-100 kDa has been found in a few species of bacteria. The 1.95 A crystal structure of the monomeric IDH revealed that it consists of two distinct domains, and its folding topology is related to the dimeric IDH. The structure of the large domain repeats a motif observed in the dimeric IDH. Such a fusional structure by domain duplication enables a single polypeptide chain to form a structure at the catalytic site that is homologous to the dimeric IDH, the catalytic site of which is located at the interface of two identical subunits.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.4051α = 90
b = 119.0229β = 99.0058
c = 128.217γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
DMmodel building
DMMultimodel building
CCP4data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-11
    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: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations