Isopropylmalate dehydrogenase in complex with NAD+

Experimental Data Snapshot

  • Resolution: 3.49 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.193 

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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, E
A, B, C, D, E, F, G, H
405Arabidopsis 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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
CA [auth G]
EA [auth H]
I [auth A]
L [auth A]
O [auth C]
CA [auth G],
EA [auth H],
I [auth A],
L [auth A],
O [auth C],
T [auth D],
V [auth D],
Z [auth E]
C21 H27 N7 O14 P2
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth E]
DA [auth G]
FA [auth H]
GA [auth H]
J [auth A]
AA [auth E],
DA [auth G],
FA [auth H],
GA [auth H],
J [auth A],
M [auth A],
P [auth C],
Q [auth C],
U [auth D],
W [auth D]
O4 S
Query on MG

Download Ideal Coordinates CCD File 
BA [auth E]
K [auth A]
N [auth A]
R [auth C]
S [auth C]
BA [auth E],
K [auth A],
N [auth A],
R [auth C],
S [auth C],
X [auth D],
Y [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 3.49 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.2α = 90
b = 132.868β = 90
c = 349.426γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data 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: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-07-06
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description