6ixn

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Current revision (10:35, 27 March 2024) (edit) (undo)
 
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<StructureSection load='6ixn' size='340' side='right'caption='[[6ixn]], [[Resolution|resolution]] 1.87&Aring;' scene=''>
<StructureSection load='6ixn' size='340' side='right'caption='[[6ixn]], [[Resolution|resolution]] 1.87&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6ixn]] 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=6IXN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IXN FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6ixn]] 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=6IXN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IXN FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.87&#8491;</td></tr>
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<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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=6ixn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ixn OCA], [https://pdbe.org/6ixn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ixn RCSB], [https://www.ebi.ac.uk/pdbsum/6ixn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ixn ProSAT]</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=6ixn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ixn OCA], [https://pdbe.org/6ixn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ixn RCSB], [https://www.ebi.ac.uk/pdbsum/6ixn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ixn ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[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>
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6ixn" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Ostta]]
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[[Category: Ostreococcus tauri]]
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[[Category: Tang, W G]]
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[[Category: Tang WG]]
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[[Category: Wang, P]]
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[[Category: Wang P]]
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[[Category: Zhu, G P]]
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[[Category: Zhu GP]]
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[[Category: Isocitrate dehydrogenase]]
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[[Category: Oxidoreductase]]
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Current revision

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

PDB ID 6ixn

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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