3D structure of E. coli Isocitrate Dehydrogenase in complex with Isocitrate, calcium(II) and thioNADP

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

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Induced Fit and the Catalytic Mechanism of Isocitrate Dehydrogenase.

Goncalves, S.Miller, S.P.Carrondo, M.A.Dean, A.M.Matias, P.M.

(2012) Biochemistry 51: 7098

  • DOI: https://doi.org/10.1021/bi300483w
  • Primary Citation of Related Structures:  
    4AJ3, 4AJA, 4AJB, 4AJC, 4AJR, 4AJS

  • PubMed Abstract: 

    NADP(+) dependent isocitrate dehydrogenase (IDH; EC belongs to a large family of α-hydroxyacid oxidative β-decarboxylases that catalyze similar three-step reactions, with dehydrogenation to an oxaloacid intermediate preceding β-decarboxylation to an enol intermediate followed by tautomerization to the final α-ketone product. A comprehensive view of the induced fit needed for catalysis is revealed on comparing the first "fully closed" crystal structures of a pseudo-Michaelis complex of wild-type Escherichia coli IDH (EcoIDH) and the "fully closed" reaction product complex of the K100M mutant with previously obtained "quasi-closed" and "open" conformations. Conserved catalytic residues, binding the nicotinamide ring of NADP(+) and the metal-bound substrate, move as rigid bodies during domain closure by a hinge motion that spans the central β-sheet in each monomer. Interactions established between Thr105 and Ser113, which flank the "phosphorylation loop", and the nicotinamide mononucleotide moiety of NADP(+) establish productive coenzyme binding. Electrostatic interactions of a Lys100-Leu103-Asn115-Glu336 tetrad play a pivotal role in assembling a catalytically competent active site. As predicted, Lys230* is positioned to deprotonate/reprotonate the α-hydroxyl in both reaction steps and Tyr160 moves into position to protonate C3 following β-decarboxylation. A proton relay from the catalytic triad Tyr160-Asp307-Lys230* connects the α-hydroxyl of isocitrate to the bulk solvent to complete the picture of the catalytic mechanism.

  • Organizational Affiliation

    Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2780 Oeiras Portugal.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADP ISOCITRATE DEHYDROGENASE416Escherichia coliMutation(s): 0 
Find proteins for P08200 (Escherichia coli (strain K12))
Explore P08200 
Go to UniProtKB:  P08200
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08200
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.01α = 90
b = 104.01β = 90
c = 149.563γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description