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| | <StructureSection load='7e2w' size='340' side='right'caption='[[7e2w]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='7e2w' size='340' side='right'caption='[[7e2w]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[7e2w]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ostta Ostta]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6ixu 6ixu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7E2W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7E2W FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7e2w]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ostreococcus_tauri Ostreococcus tauri]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6ixu 6ixu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7E2W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7E2W FirstGlance]. <br> |
| - | </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=ICT:ISOCITRIC+ACID'>ICT</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</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]] 1.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6ixl|6ixl]], [[6ixt|6ixt]], [[6ixn|6ixn]]</div></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=ICT:ISOCITRIC+ACID'>ICT</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">IDH, Ot_13g02940, BE221DRAFT_192402 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70448 OSTTA])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Isocitrate_dehydrogenase_(NAD(+)) Isocitrate dehydrogenase (NAD(+))], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.41 1.1.1.41] </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=7e2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e2w OCA], [https://pdbe.org/7e2w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e2w RCSB], [https://www.ebi.ac.uk/pdbsum/7e2w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e2w 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=7e2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e2w OCA], [https://pdbe.org/7e2w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e2w RCSB], [https://www.ebi.ac.uk/pdbsum/7e2w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e2w ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[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>
| + | [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> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[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]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
7e2w is a 4 chain structure with sequence from Ostreococcus tauri. This structure supersedes the now removed PDB entry 6ixu. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.8Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
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).[1]
Publication Abstract from PubMed
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[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Tang WG, Song P, Cao ZY, Wang P, Zhu GP. A unique homodimeric NAD(+)-linked isocitrate dehydrogenase from the smallest autotrophic eukaryote Ostreococcus tauri. FASEB J. 2015 Jun;29(6):2462-72. doi: 10.1096/fj.14-257014. Epub 2015 Feb 27. PMID:25724193 doi:http://dx.doi.org/10.1096/fj.14-257014
- ↑ Tang W, Wu M, Qin N, Liu L, Meng R, Wang C, Wang P, Zang J, Zhu G. Crystal structures of NAD(+)-linked isocitrate dehydrogenase from the green alga Ostreococcus tauri and its evolutionary relationship with eukaryotic NADP(+)-linked homologs. Arch Biochem Biophys. 2021 May 3;708:108898. doi: 10.1016/j.abb.2021.108898. PMID:33957092 doi:http://dx.doi.org/10.1016/j.abb.2021.108898
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