Isopropylmalate dehydrogenase in complex with isopropylmalate

Experimental Data Snapshot

  • Resolution: 1.93 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

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Structure and Mechanism of Isopropylmalate Dehydrogenase from Arabidopsis thaliana: INSIGHTS ON LEUCINE AND ALIPHATIC GLUCOSINOLATE BIOSYNTHESIS.

Lee, S.G.Nwumeh, R.Jez, J.M.

(2016) J Biol Chem 291: 13421-13430

  • DOI: https://doi.org/10.1074/jbc.M116.730358
  • Primary Citation of Related Structures:  
    5J32, 5J33, 5J34

  • PubMed Abstract: 

    Isopropylmalate dehydrogenase (IPMDH) and 3-(2'-methylthio)ethylmalate dehydrogenase catalyze the oxidative decarboxylation of different β-hydroxyacids in the leucine- and methionine-derived glucosinolate biosynthesis pathways, respectively, in plants. Evolution of the glucosinolate biosynthetic enzyme from IPMDH results from a single amino acid substitution that alters substrate specificity. Here, we present the x-ray crystal structures of Arabidopsis thaliana IPMDH2 (AtIPMDH2) in complex with either isopropylmalate and Mg(2+) or NAD(+) These structures reveal conformational changes that occur upon ligand binding and provide insight on the active site of the enzyme. The x-ray structures and kinetic analysis of site-directed mutants are consistent with a chemical mechanism in which Lys-232 activates a water molecule for catalysis. Structural analysis of the AtIPMDH2 K232M mutant and isothermal titration calorimetry supports a key role of Lys-232 in the reaction mechanism. This study suggests that IPMDH-like enzymes in both leucine and glucosinolate biosynthesis pathways use a common mechanism and that members of the β-hydroxyacid reductive decarboxylase family employ different active site features for similar reactions.

  • Organizational Affiliation

    From the Department of Biology, Washington University, St. Louis, Missouri 63130.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-isopropylmalate dehydrogenase 2, chloroplastic
A, B, C, D
403Arabidopsis thalianaMutation(s): 0 
Gene Names: IMDH2IMDHAt1g80560T21F11.11
Find proteins for P93832 (Arabidopsis thaliana)
Explore P93832 
Go to UniProtKB:  P93832
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP93832
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.93 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.059α = 90
b = 49.622β = 105.44
c = 158.969γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-0904215

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-11
    Type: Initial release
  • Version 1.1: 2016-05-18
    Changes: Database references
  • Version 1.2: 2016-07-06
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Advisory, Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description