Structure and Mechanism of Isopropylmalate Dehydrogenase from Arabidopsis thaliana: Insights on Leucine and Aliphatic Glucosinolate Biosynthesis
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 Mg2+ 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. Furthermore, 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.
- Authors:
-
- Washington Univ., St. Louis, MO (United States)
- Publication Date:
- Research Org.:
- Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
- Sponsoring Org.:
- National Science Foundation (NSF); USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1267478
- Grant/Contract Number:
- MCB-0904215; AC02–06CH11357
- Resource Type:
- Journal Article: Accepted Manuscript
- Journal Name:
- Journal of Biological Chemistry
- Additional Journal Information:
- Journal Volume: 291; Journal Issue: 26; Journal ID: ISSN 0021-9258
- Publisher:
- American Society for Biochemistry and Molecular Biology
- Country of Publication:
- United States
- Language:
- ENGLISH
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; enzyme; plant biochemistry; protein evolution; protein structure; x-ray crystallography; reaction mechanism
Citation Formats
Lee, Soon Goo, Nwumeh, Ronald, and Jez, Joseph M. Structure and Mechanism of Isopropylmalate Dehydrogenase from Arabidopsis thaliana: Insights on Leucine and Aliphatic Glucosinolate Biosynthesis. United States: N. p., 2016.
Web. doi:10.1074/jbc.M116.730358.
Lee, Soon Goo, Nwumeh, Ronald, & Jez, Joseph M. Structure and Mechanism of Isopropylmalate Dehydrogenase from Arabidopsis thaliana: Insights on Leucine and Aliphatic Glucosinolate Biosynthesis. United States. https://doi.org/10.1074/jbc.M116.730358
Lee, Soon Goo, Nwumeh, Ronald, and Jez, Joseph M. 2016.
"Structure and Mechanism of Isopropylmalate Dehydrogenase from Arabidopsis thaliana: Insights on Leucine and Aliphatic Glucosinolate Biosynthesis". United States. https://doi.org/10.1074/jbc.M116.730358. https://www.osti.gov/servlets/purl/1267478.
@article{osti_1267478,
title = {Structure and Mechanism of Isopropylmalate Dehydrogenase from Arabidopsis thaliana: Insights on Leucine and Aliphatic Glucosinolate Biosynthesis},
author = {Lee, Soon Goo and Nwumeh, Ronald and Jez, Joseph M.},
abstractNote = {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 Mg2+ 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. Furthermore, 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.},
doi = {10.1074/jbc.M116.730358},
url = {https://www.osti.gov/biblio/1267478},
journal = {Journal of Biological Chemistry},
issn = {0021-9258},
number = 26,
volume = 291,
place = {United States},
year = {Mon May 02 00:00:00 EDT 2016},
month = {Mon May 02 00:00:00 EDT 2016}
}
Web of Science
Works referenced in this record:
Crystal structures of Escherichia coli and Salmonella typhimurium 3-isopropylmalate dehydrogenase and comparison with their thermophilic counterpart from Thermus thermophilus
journal, March 1997
- Wallon, Gerlind; Kryger, Gitay; Lovett, Susan T.
- Journal of Molecular Biology, Vol. 266, Issue 5
Structure of 3–isopropylmalate dehydrogenase in complex with NAD+: ligand–induced loop closing and mechanism for cofactor specificity
journal, November 1994
- Hurley, James H.; Dean, Antony M.
- Structure, Vol. 2, Issue 11
A Lysine-Tyrosine Pair Carries Out Acid−Base Chemistry in the Metal Ion-Dependent Pyridine Dinucleotide-Linked β-Hydroxyacid Oxidative Decarboxylases †
journal, April 2009
- Aktas, Deniz F.; Cook, Paul F.
- Biochemistry, Vol. 48, Issue 16
Crystal Structure of Tetrameric Homoisocitrate Dehydrogenase from an Extreme Thermophile, Thermus thermophilus: Involvement of Hydrophobic Dimer-Dimer Interaction in Extremely High Thermotolerance
journal, September 2005
- Miyazaki, J.; Asada, K.; Fushinobu, S.
- Journal of Bacteriology, Vol. 187, Issue 19
Arabidopsis Branched-Chain Aminotransferase 3 Functions in Both Amino Acid and Glucosinolate Biosynthesis
journal, December 2007
- Knill, Tanja; Schuster, Joachim; Reichelt, Michael
- Plant Physiology, Vol. 146, Issue 3
Functional characterization of Arabidopsis thaliana isopropylmalate dehydrogenases reveals their important roles in gametophyte development
journal, September 2010
- He, Yan; Chen, Liqun; Zhou, Yuan
- New Phytologist, Vol. 189, Issue 1
Features and development of Coot
journal, March 2010
- Emsley, P.; Lohkamp, B.; Scott, W. G.
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
Cloning and expression analysis of β-isopropylmalate dehydrogenase from potato
journal, January 1993
- Jackson, Stephen D.; Sonnewald, Uwe; Willmitzer, Lothar
- Molecular and General Genetics MGG, Vol. 236-236, Issue 2-3
Three-dimensional structure of a highly thermostable enzyme, 3-isopropylmalate dehydrogenase of Thermus thermophilus at 2.2 Å resolution
journal, December 1991
- Imada, Katsumi; Sato, Mamoru; Tanaka, Nobuo
- Journal of Molecular Biology, Vol. 222, Issue 3
Dual Role of the Active Site Residues of Thermus thermophilus 3-Isopropylmalate Dehydrogenase: Chemical Catalysis and Domain Closure
journal, January 2016
- Gráczer, Éva; Szimler, Tamás; Garamszegi, Anita
- Biochemistry, Vol. 55, Issue 3
PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010
- Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
Glucosinolate structures in evolution
journal, May 2012
- Agerbirk, Niels; Olsen, Carl Erik
- Phytochemistry, Vol. 77
MAM3 Catalyzes the Formation of All Aliphatic Glucosinolate Chain Lengths in Arabidopsis
journal, March 2007
- Textor, Susanne; de Kraker, Jan-Willem; Hause, Bettina
- Plant Physiology, Vol. 144, Issue 1
Tyr-139 in Thermus thermophilus 3-isopropylmalate dehydrogenase is involved in catalytic function
journal, October 1993
- Miyazaki, Kentaro; Oshima, Tairo
- FEBS Letters, Vol. 332, Issue 1-2
Seeing double: gene duplication and diversification in plant secondary metabolism
journal, September 2005
- Ober, Dietrich
- Trends in Plant Science, Vol. 10, Issue 9
Natural diversity and adaptation in plant secondary metabolism
journal, June 2011
- Kroymann, Juergen
- Current Opinion in Plant Biology, Vol. 14, Issue 3
A Catalytic Triad Is Responsible for Acid−Base Chemistry in the Ascaris suum NAD−Malic Enzyme †
journal, March 2005
- Karsten, William E.; Liu, Dali; Rao, G. S. Jagannatha
- Biochemistry, Vol. 44, Issue 9
Biosynthesis of methionine-derived glucosinolates in Arabidopsis thaliana : recombinant expression and characterization of methylthioalkylmalate synthase, the condensing enzyme of the chain-elongation cycle
journal, April 2004
- Textor, Susanne; Bartram, Stefan; Kroymann, J�rgen
- Planta, Vol. 218, Issue 6
NMRPipe: A multidimensional spectral processing system based on UNIX pipes
journal, November 1995
- Delaglio, Frank; Grzesiek, Stephan; Vuister, GeertenW.
- Journal of Biomolecular NMR, Vol. 6, Issue 3
Biology and Biochemistry of Glucosinolates
journal, June 2006
- Halkier, Barbara Ann; Gershenzon, Jonathan
- Annual Review of Plant Biology, Vol. 57, Issue 1
Glutamate 190 Is a General Acid Catalyst in the 6-Phosphogluconate-Dehydrogenase-Catalyzed Reaction †
journal, November 1998
- Karsten, William E.; Chooback, Lilian; Cook, Paul F.
- Biochemistry, Vol. 37, Issue 45
Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 å resolution: the role of Glu88 in the unique substrate-recognition mechanism
journal, August 1998
- Imada, Katsumi; Inagaki, Kenji; Matsunami, Hideyuki
- Structure, Vol. 6, Issue 8
BRANCHED-CHAIN AMINOTRANSFERASE4 Is Part of the Chain Elongation Pathway in the Biosynthesis of Methionine-Derived Glucosinolates in Arabidopsis
journal, October 2006
- Schuster, Joachim; Knill, Tanja; Reichelt, Michael
- The Plant Cell, Vol. 18, Issue 10
Allosteric Motions in Structures of Yeast NAD + -specific Isocitrate Dehydrogenase
journal, February 2008
- Taylor, Alexander B.; Hu, Gang; Hart, P. John
- Journal of Biological Chemistry, Vol. 283, Issue 16
Ligand-Induced Changes in the Conformation of 3-Isopropylmalate Dehydrogenase from Thermus thermophilus
journal, October 1995
- Kadono, Shojiro; Sakurai, Masahiro; Moriyama, Hideaki
- The Journal of Biochemistry, Vol. 118, Issue 4
Structural and Functional Evolution of Isopropylmalate Dehydrogenases in the Leucine and Glucosinolate Pathways of Arabidopsis thaliana
journal, June 2011
- He, Yan; Galant, Ashley; Pang, Qiuying
- Journal of Biological Chemistry, Vol. 286, Issue 33
Cloning of a cDNA for rape chloroplast 3-isopropylmalate dehydrogenase by genetic complementation in yeast
journal, February 1992
- Ellerstr�m, Mats; Josefsson, Lars -G�ran; Rask, Lars
- Plant Molecular Biology, Vol. 18, Issue 3
Cloning of cDNAs Encoding Isopropylmalate Dehydrogenase from Arabidopsis thaliana and Accumulation Patterns of Their Transcripts
journal, January 2005
- Nozawa, Akira; Takano, Junpei; Miwa, Kyoko
- Bioscience, Biotechnology, and Biochemistry, Vol. 69, Issue 4
A redox-active isopropylmalate dehydrogenase functions in the biosynthesis of glucosinolates and leucine in Arabidopsis
journal, November 2009
- He, Yan; Mawhinney, Thomas P.; Preuss, Mary L.
- The Plant Journal, Vol. 60, Issue 4
Phaser crystallographic software
journal, July 2007
- McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
- Journal of Applied Crystallography, Vol. 40, Issue 4