5J32

Isopropylmalate dehydrogenase in complex with isopropylmalate

Summary for 5J32

• Entry DOI: 10.2210/pdb5j32/pdb
• Descriptor: 3-isopropylmalate dehydrogenase 2, chloroplastic, MAGNESIUM ION, 3-ISOPROPYLMALIC ACID, ... (4 entities in total)
• Functional Keywords: dehydrogenase, leucine biosynthesis, glucosinolate biosynthesis, oxidoreductase
• Biological source: Arabidopsis thaliana (Mouse-ear cress)
• Total number of polymer chains: 4
• Total formula weight: 173618.23

Authors

Jez, J.M.,Lee, S.G. (deposition date: 2016-03-30, release date: 2016-05-11, Last modification date: 2023-09-27)

Primary citation

Lee, S.G.,Nwumeh, R.,Jez, J.M.
Structure and Mechanism of Isopropylmalate Dehydrogenase from Arabidopsis thaliana: INSIGHTS ON LEUCINE AND ALIPHATIC GLUCOSINOLATE BIOSYNTHESIS.
J.Biol.Chem., 291:13421-13430, 2016

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.

PubMed: 27137927
DOI: 10.1074/jbc.M116.730358

Experimental method

X-RAY DIFFRACTION (1.933 Å)