5J33

Isopropylmalate dehydrogenase in complex with NAD+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 


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Literature

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: 10.1074/jbc.M116.730358
  • Primary Citation of Related Structures:  
    5J33, 5J32, 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 ...

    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 jjez@wustl.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-isopropylmalate dehydrogenase 2, chloroplasticA, B, C, D, E, F, G, H405Arabidopsis thalianaMutation(s): 0 
Gene Names: IMDH2IMDHAt1g80560T21F11.11IMD2IPMDH2
EC: 1.1.1.85
UniProt
Find proteins for P93832 (Arabidopsis thaliana)
Explore P93832 
Go to UniProtKB:  P93832
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
CA [auth G], EA [auth H], I [auth A], L [auth A], O [auth C], T [auth D], V [auth D], Z [auth E]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth E] , DA [auth G] , FA [auth H] , GA [auth H] , J [auth A] , M [auth A] , P [auth C] , Q [auth C] , 
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]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth E], K [auth A], N [auth A], R [auth C], S [auth C], X [auth D], Y [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2016-03-30 
  • Released Date: 2016-05-18 
  • Deposition Author(s): Jez, J.M., Lee, S.G.

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