PDBsum entry 2b0t

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protein metals links
Oxidoreductase PDB id
Protein chain
735 a.a. *
Waters ×474
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Structure of monomeric NADP isocitrate dehydrogenase
Structure: NADP isocitrate dehydrogenase. Chain: a. Synonym: oxalosuccinate decarboxylase, idh. Ec:
Source: Corynebacterium glutamicum. Organism_taxid: 1718
1.75Å     R-factor:   0.200     R-free:   0.230
Authors: F.Imabayashi,S.Aich,L.Prasad,L.T.Delbaere
Key ref:
F.Imabayashi et al. (2006). Substrate-free structure of a monomeric NADP isocitrate dehydrogenase: an open conformation phylogenetic relationship of isocitrate dehydrogenase. Proteins, 63, 100-112. PubMed id: 16416443 DOI: 10.1002/prot.20867
14-Sep-05     Release date:   31-Jan-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P50216  (IDH_CORGL) -  Isocitrate dehydrogenase [NADP]
738 a.a.
735 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Isocitrate dehydrogenase (NADP(+)).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Citric acid cycle
      Reaction: Isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH
+ NADP(+)
= 2-oxoglutarate
+ CO(2)
      Cofactor: Mn(2+) or Mg(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     4 terms  


DOI no: 10.1002/prot.20867 Proteins 63:100-112 (2006)
PubMed id: 16416443  
Substrate-free structure of a monomeric NADP isocitrate dehydrogenase: an open conformation phylogenetic relationship of isocitrate dehydrogenase.
F.Imabayashi, S.Aich, L.Prasad, L.T.Delbaere.
Both monomeric and dimeric NADP+-dependent isocitrate dehydrogenase (IDH) belong to the metal-dependent beta-decarboxylating dehydrogenase family and catalyze the oxidative decarboxylation from 2R,3S-isocitrate to yield 2-oxoglutarate, CO2, and NADPH. It is important to solve the structures of IDHs from various species to correlate with its function and evolutionary significance. So far, only two crystal structures of substrate/cofactor-bound (isocitrate/NADP) NADP+-dependent monomeric IDH from Azotobacter vinelandii (AvIDH) have been solved. Herein, we report for the first time the substrate/cofactor-free structure of a monomeric NADP+-dependent IDH from Corynebacterium glutamicum (CgIDH) in the presence of Mg2+. The 1.75 A structure of CgIDH-Mg2+ showed a distinct open conformation in contrast to the closed conformation of AvIDH-isocitrate/NADP+ complexes. Fluorescence studies on CgIDH in the presence of isocitrate/or NADP+ suggest the presence of low energy barrier conformers. In CgIDH, the amino acid residues corresponding to the Escherichia coli IDH phosphorylation-loop are alpha-helical compared with the more flexible random-coil region in the E. coli protein where IDH activation is controlled by phosphorylation. This more structured region supports the idea that activation of CgIDH is not controlled by phosphorylation. Monomeric NADP+-specific IDHs have been identified from about 50 different bacterial species, such as proteobacteria, actinobacteria, and planctomycetes, whereas, dimeric NADP+-dependent IDHs are diversified in both prokaryotes and eukaryotes. We have constructed a phylogenetic tree based on amino acid sequences of all bacterial monomeric NADP+-dependent IDHs and also another one with specifically chosen species which either contains both monomeric and dimeric NADP+-dependent IDHs or have monomeric NADP+-dependent, as well as NAD+-dependent IDHs. This is done to examine evolutionary relationships.
  Selected figure(s)  
Figure 2.
Figure 2. Stereo diagram of the coordinating geometry of Mg^2+ in the CgIDH-Mg^2+ structure. Three Asp residues (red) and two water molecules (blue spheres) coordinate Mg^2+ (pink sphere) in an octahedral manner.
Figure 8.
Figure 8. Stereo diagrams of the coordination geometries for the divalent metal cations in the structures of AvIDH-isocitrate-Mn^2+. The coordinating residues are drawn in green, whereas isocitrate-Mn^2+ are drawn in yellow. The blue spheres represent water molecules.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 63, 100-112) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19284579 J.E.Butler, N.D.Young, and D.R.Lovley (2009).
Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative fenomics of six Geobacteraceae species.
  BMC Genomics, 10, 103.  
  19052369 G.N.Hatzopoulos, G.Kefala, and J.Mueller-Dieckmann (2008).
Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of isocitrate dehydrogenase 2 (Rv0066c) from Mycobacterium tuberculosis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1139-1142.  
18552125 Y.Peng, C.Zhong, W.Huang, and J.Ding (2008).
Structural studies of Saccharomyces cerevesiae mitochondrial NADP-dependent isocitrate dehydrogenase in different enzymatic states reveal substantial conformational changes during the catalytic reaction.
  Protein Sci, 17, 1542-1554.
PDB codes: 2qfv 2qfw 2qfx 2qfy
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