5j33: Difference between revisions
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New page: '''Unreleased structure''' The entry 5j33 is ON HOLD until Paper Publication Authors: Jez, J.M., Lee, S.G. Description: Isopropylmalate dehydrogenase in complex with NAD+ [[Category: U... |
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==Isopropylmalate dehydrogenase in complex with NAD+== | |||
<StructureSection load='5j33' size='340' side='right'caption='[[5j33]], [[Resolution|resolution]] 3.49Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5j33]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J33 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J33 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.492Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5j33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j33 OCA], [https://pdbe.org/5j33 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j33 RCSB], [https://www.ebi.ac.uk/pdbsum/5j33 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j33 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/LEU32_ARATH LEU32_ARATH] Catalyzes the oxidation of 3-carboxy-2-hydroxy-4-methylpentanoate (3-isopropylmalate) to 3-carboxy-4-methyl-2-oxopentanoate. The product decarboxylates to 4-methyl-2 oxopentanoate. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Isopropylmalate dehydrogenase (IPMDH) and 3-(2'-methylthio)ethylmalate dehydrogenase catalyze the oxidative decarboxylation of different beta-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 Lys232 activates a water molecule for catalysis. Structural analysis of the AtIPMDH2 K232M mutant and isothermal titration calorimetry supports a key role of Lys232 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 beta-hydroxyacid reductive decarboxylase family employ different active site features for similar reactions. | |||
Structure and Mechanism of Isopropylmalate Dehydrogenase from Arabidopsis thaliana: Insights on Leucine and Aliphatic Glucosinolate Biosynthesis.,Lee SG, Nwumeh R, Jez JM J Biol Chem. 2016 May 2. pii: jbc.M116.730358. PMID:27137927<ref>PMID:27137927</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Jez | <div class="pdbe-citations 5j33" style="background-color:#fffaf0;"></div> | ||
[[Category: Lee | |||
==See Also== | |||
*[[Isopropylmalate dehydrogenase|Isopropylmalate dehydrogenase]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Arabidopsis thaliana]] | |||
[[Category: Large Structures]] | |||
[[Category: Jez JM]] | |||
[[Category: Lee SG]] | |||
Latest revision as of 10:43, 6 September 2023
Isopropylmalate dehydrogenase in complex with NAD+
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