1ITW

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 

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This is version 1.3 of the entry. See complete history. 


Literature

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: 10.1016/s0969-2126(02)00904-8
  • Primary Citation of Related Structures:  
    1ITW

  • 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 prokary ...

    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.

    Related Citations: 
    • Crystallization and preliminary X-ray diffraction studies of monomeric isocitrate dehydrogenase by the MAD method using Mn atoms
      Yasutake, Y., Watanabe, S., Yao, M., Takada, Y., Fukunaga, N., Tanaka, I.
      (2001) Acta Crystallogr D Biol Crystallogr 57: 1682
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isocitrate dehydrogenase A, B, C, D741Azotobacter vinelandiiMutation(s): 0 
Gene Names: icd
EC: 1.1.1.42
Find proteins for P16100 (Azotobacter vinelandii)
Explore P16100 
Go to UniProtKB:  P16100
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
SHARPphasing
SHELXSphasing
AMoREphasing
DMmodel building
DMMultimodel building
CNSrefinement
CCP4data scaling
DMphasing
DMMultiphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • 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