5YZI | pdb_00005yzi

Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase complexed with Cadmium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 
    0.231 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

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Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

NADP+-dependent cytosolic isocitrate dehydrogenase provides NADPH in the presence of cadmium due to the moderate chelating effect of glutathione.

Cho, H.J.Cho, H.Y.Park, J.W.Kwon, O.S.Lee, H.S.Huh, T.L.Kang, B.S.

(2018) J Biol Inorg Chem 23: 849-860

  • DOI: https://doi.org/10.1007/s00775-018-1581-5
  • Primary Citation of Related Structures:  
    5YZH, 5YZI

  • PubMed Abstract: 

    Cadmium (Cd 2+ ) is toxic to living organisms because it causes the malfunction of essential proteins and induces oxidative stress. NADP + -dependent cytosolic isocitrate dehydrogenase (IDH) provides reducing energy to counteract oxidative stress via oxidative decarboxylation of isocitrate. Intriguingly, the effects of Cd 2+ on the activity of IDH are both positive and negative, and to understand the molecular basis, we determined the crystal structure of NADP + -dependent cytosolic IDH in the presence of Cd 2+ . The structure includes two Cd 2+ ions, one coordinated by active site residues and another near a cysteine residue. Cd 2+ presumably inactivates IDH due to its high affinity for thiols, leading to a covalent enzyme modification. However, Cd 2+ also activates IDH by providing a divalent cation required for catalytic activity. Inactivation of IDH by Cd 2+ is less effective when the enzyme is activated with Cd 2+ than Mg 2+ . Although reducing agents cannot restore activity following inactivation by Cd 2+ , they can maintain IDH activity by chelating Cd 2+ . Glutathione, a cellular sulphydryl reductant, has a moderate affinity for Cd 2+ , allowing IDH to be activated with residual Cd 2+ , unlike dithiothreitol, which has a much higher affinity. In the presence of Cd 2+ -consuming cellular antioxidants, cells must continually supply reductants to protect against oxidative stress. The ability of IDH to utilise Cd 2+ to generate NADPH could allow cells to protect themselves against Cd 2+ .


  • Organizational Affiliation

    School of Life Science and Biotechnology, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, South Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isocitrate dehydrogenase [NADP] cytoplasmic
A, B
414Mus musculusMutation(s): 0 
Gene Names: Idh1
EC: 1.1.1.42
UniProt & NIH Common Fund Data Resources
Find proteins for O88844 (Mus musculus)
Explore O88844 
Go to UniProtKB:  O88844
IMPC:  MGI:96413
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO88844
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.246α = 90
b = 91.428β = 113.65
c = 109.724γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2019-03-20
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references