5h3f: Difference between revisions

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 ==Crystal structure of mouse isocitrate dehydrogenases 2 complexed with isocitrate==
-<StructureSection load='5h3f' size='340' side='right' caption='[[5h3f]], [[Resolution|resolution]] 3.29&Aring;' scene=''>
+<StructureSection load='5h3f' size='340' side='right'caption='[[5h3f]], [[Resolution|resolution]] 3.29&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5h3f]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H3F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H3F FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5h3f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H3F FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ICT:ISOCITRIC+ACID'>ICT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 3.29&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5h3e|5h3e]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ICT:ISOCITRIC+ACID'>ICT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase_(NADP(+)) Isocitrate dehydrogenase (NADP(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.42 1.1.1.42] </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=5h3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h3f OCA], [https://pdbe.org/5h3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h3f RCSB], [https://www.ebi.ac.uk/pdbsum/5h3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h3f 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=5h3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h3f OCA], [http://pdbe.org/5h3f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h3f RCSB], [http://www.ebi.ac.uk/pdbsum/5h3f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h3f ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/IDHP_MOUSE IDHP_MOUSE]] Plays a role in intermediary metabolism and energy production. It may tightly associate or interact with the pyruvate dehydrogenase complex.
+[https://www.uniprot.org/uniprot/IDHP_MOUSE IDHP_MOUSE] Plays a role in intermediary metabolism and energy production. It may tightly associate or interact with the pyruvate dehydrogenase complex.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Mitochondrial isocitrate dehydrogenase 2 (IDH2) converts NADP+ to NADPH and promotes regeneration of reduced glutathione (GSH) by supplying NADPH to glutathione reductase or thioredoxin reductase. We have previously shown that under calorie restriction, mitochondrial deacetylase Sirt3 deacetylates and activates IDH2, thereby regulating the mitochondrial glutathione antioxidant defense system in mice. To investigate the regulatory mechanism of mIDH2 (mouse mitochondrial IDH2), we used lysine-to-glutamine (KQ) mutants to mimic acetylated lysines and screened 15 KQ mutants. Among these mutants, the activities of the K256Q and K413Q proteins were less than 50% of the wild-type value. We then solved the crystal structures of the wild-type mIDH2 and the K256Q mutant proteins, revealing conformational changes in the substrate-binding pocket. Structural data suggested that positively charged Lys256 was important in stabilizing the pocket because it repelled a lysine cluster on the other side. Glutamine (or acetylated lysine) was neutral and thus caused the pocket size to decrease, which might be the main reason for the lower activity of the K256Q mutant. Together, our data provide the first structure of an acetylation mimic of mIDH2 and new insights into the regulatory mechanism of acetylation of mIDH2.
+Studies on the regulatory mechanism of isocitrate dehydrogenase 2 using acetylation mimics.,Xu Y, Liu L, Nakamura A, Someya S, Miyakawa T, Tanokura M Sci Rep. 2017 Aug 29;7(1):9785. doi: 10.1038/s41598-017-10337-7. PMID:28852116<ref>PMID:28852116</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 5h3f" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Isocitrate dehydrogenase 3D structures|Isocitrate dehydrogenase 3D structures]]
+== References ==
+<references/>
 __TOC__
 </StructureSection>
-[[Category: Liu, L]]
+[[Category: Large Structures]]
-[[Category: Miyakawa, T]]
+[[Category: Mus musculus]]
-[[Category: Nakamura, A]]
+[[Category: Liu L]]
-[[Category: Tanokura, M]]
+[[Category: Miyakawa T]]
-[[Category: Xu, Y]]
+[[Category: Nakamura A]]
-[[Category: Nadp dependent isocitrate dehydrogenases 2]]
+[[Category: Tanokura M]]
-[[Category: Oxidoreductase]]
+[[Category: Xu Y]]