5YZH

Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: 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 ...

    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. bskang2@knu.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isocitrate dehydrogenase [NADP] cytoplasmicA, B414Mus 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.372α = 90
b = 91.289β = 113.34
c = 109.381γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2017-12-14 
  • Released Date: 2018-07-04 
  • Deposition Author(s): Cho, H.J., Kang, B.S.
  • This entry supersedes: 2CMJ

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