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6ixt

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Crystal structure of isocitrate dehydrogenase from Ostreococcus tauri in complex with NAD+ and Mg2+

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Categories: Large Structures | Ostreococcus tauri | Tang WG | Wang P | Zhu GP

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 <StructureSection load='6ixt' size='340' side='right'caption='[[6ixt]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6ixt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ostta Ostta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IXT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6ixt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ostreococcus_tauri Ostreococcus tauri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IXT FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.78&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BE221DRAFT_192402 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70448 OSTTA])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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=6ixt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ixt OCA], [https://pdbe.org/6ixt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ixt RCSB], [https://www.ebi.ac.uk/pdbsum/6ixt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ixt ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/IDH_OSTTA IDH_OSTTA] Performs an essential role in the oxidative function of the tricarboxylic acid cycle and respiration (Probable). Catalyzes the decarboxylation of isocitrate to produce 2-oxoglutarate and generate NADH to provide electrons for energy production (Probable).<ref>PMID:25724193</ref>
-NAD(+)-linked isocitrate dehydrogenases (NAD-IDHs) catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Previously, we identified a novel phylogenetic clade including NAD-IDHs from several algae in the type II subfamily, represented by homodimeric NAD-IDH from Ostreococcus tauri (OtIDH). However, due to its lack of a crystalline structure, the molecular mechanisms of the ligand binding and catalysis of OtIDH are little known. Here, we elucidate four high-resolution crystal structures of OtIDH in a ligand-free and various ligand-bound forms that capture at least three states in the catalytic cycle: open, semi-closed, and fully closed. Our results indicate that OtIDH shows several novel interactions with NAD(+), unlike type I NAD-IDHs, as well as a strictly conserved substrate binding mode that is similar to other homologs. The central roles of Lys283' in dual coenzyme recognition and Lys234 in catalysis were also revealed. In addition, the crystal structures obtained here also allow us to understand the catalytic mechanism. As expected, structural comparisons reveal that OtIDH has a very high structural similarity to eukaryotic NADP(+)-linked IDHs (NADP-IDHs) within the type II subfamily rather than with the previously reported NAD-IDHs within the type I subfamily. It has also been demonstrated that OtIDH exhibits substantial conformation changes upon ligand binding, similar to eukaryotic NADP-IDHs. These results unambiguously support our hypothesis that OtIDH and OtIDH-like homologs are possible evolutionary ancestors of eukaryotic NADP-IDHs in type II subfamily.
-Crystal structures of NAD(+)-linked isocitrate dehydrogenase from the green alga Ostreococcus tauri and its evolutionary relationship with eukaryotic NADP(+)-linked homologs.,Tang W, Wu M, Qin N, Liu L, Meng R, Wang C, Wang P, Zang J, Zhu G Arch Biochem Biophys. 2021 May 3;708:108898. doi: 10.1016/j.abb.2021.108898. PMID:33957092<ref>PMID:33957092</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 6ixt" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 25: / Line 18: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Ostta]]
+[[Category: Ostreococcus tauri]]
-[[Category: Tang, W G]]
+[[Category: Tang WG]]
-[[Category: Wang, P]]
+[[Category: Wang P]]
-[[Category: Zhu, G P]]
+[[Category: Zhu GP]]
-[[Category: Isocitrate dehydrogenase nad+]]
-[[Category: Oxidoreductase]]

6ixt

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Crystal structure of isocitrate dehydrogenase from Ostreococcus tauri in complex with NAD+ and Mg2+

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Function

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