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| | ==Isopropylmalate dehydrogenase K232M mutant== | | ==Isopropylmalate dehydrogenase K232M mutant== |
| - | <StructureSection load='5j34' size='340' side='right' caption='[[5j34]], [[Resolution|resolution]] 1.83Å' scene=''> | + | <StructureSection load='5j34' size='340' side='right'caption='[[5j34]], [[Resolution|resolution]] 1.83Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5j34]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J34 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J34 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5j34]] is a 4 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=5J34 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J34 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.827Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5j33|5j33]], [[5j32|5j32]]</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=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-isopropylmalate_dehydrogenase 3-isopropylmalate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.85 1.1.1.85] </span></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=5j34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j34 OCA], [https://pdbe.org/5j34 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j34 RCSB], [https://www.ebi.ac.uk/pdbsum/5j34 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j34 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5j34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j34 OCA], [http://pdbe.org/5j34 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j34 RCSB], [http://www.ebi.ac.uk/pdbsum/5j34 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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. | + | [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.
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| - | 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>
| + | ==See Also== |
| - | | + | *[[Isopropylmalate dehydrogenase|Isopropylmalate dehydrogenase]] |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 5j34" style="background-color:#fffaf0;"></div>
| + | |
| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 3-isopropylmalate dehydrogenase]] | + | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Jez, J M]] | + | [[Category: Large Structures]] |
| - | [[Category: Lee, S G]] | + | [[Category: Jez JM]] |
| - | [[Category: Dehydrogenase]] | + | [[Category: Lee SG]] |
| - | [[Category: Glucosinolate biosynthesis]]
| + | |
| - | [[Category: Leucine biosynthesis]]
| + | |
| - | [[Category: Oxidoreductase]]
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