3blv: Difference between revisions

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-[[Image:3blv.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_3blv", creates the "Structure Box" on the page.
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-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_3blv|  PDB=3blv  |  SCENE=  }}
-'''Yeast Isocitrate Dehydrogenase with Citrate Bound in the Regulatory Subunits'''
+==Yeast Isocitrate Dehydrogenase with Citrate Bound in the Regulatory Subunits==
+<StructureSection load='3blv' size='340' side='right'caption='[[3blv]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3blv]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BLV FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.2&#8491;</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=MSE:SELENOMETHIONINE'>MSE</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=3blv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blv OCA], [https://pdbe.org/3blv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3blv RCSB], [https://www.ebi.ac.uk/pdbsum/3blv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3blv ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/IDH1_YEAST IDH1_YEAST] Performs an essential role in the oxidative function of the citric acid cycle. Also binds RNA; specifically to the 5'-untranslated leaders of mitochondrial mRNAs.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bl/3blv_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3blv ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Mitochondrial NAD(+)-specific isocitrate dehydrogenases (IDHs) are key regulators of flux through biosynthetic and oxidative pathways in response to cellular energy levels. Here we present the first structures of a eukaryotic member of this enzyme family, the allosteric, hetero-octameric, NAD(+)-specific IDH from yeast in three forms: 1) without ligands, 2) with bound analog citrate, and 3) with bound citrate + AMP. The structures reveal the molecular basis for ligand binding to homologous but distinct regulatory and catalytic sites positioned at the interfaces between IDH1 and IDH2 subunits and define pathways of communication between heterodimers and heterotetramers in the hetero-octamer. Disulfide bonds observed at the heterotetrameric interfaces in the unliganded IDH hetero-octamer are reduced in the ligand-bound forms, suggesting a redox regulatory mechanism that may be analogous to the "on-off" regulation of non-allosteric bacterial IDHs via phosphorylation. The results strongly suggest that eukaryotic IDH enzymes are exquisitely tuned to ensure that allosteric activation occurs only when concentrations of isocitrate are elevated.
-==Overview==
+Allosteric motions in structures of yeast NAD+-specific isocitrate dehydrogenase.,Taylor AB, Hu G, Hart PJ, McAlister-Henn L J Biol Chem. 2008 Apr 18;283(16):10872-80. Epub 2008 Feb 6. PMID:18256028<ref>PMID:18256028</ref>
-Mitochondrial NAD(+)-specific isocitrate dehydrogenases (IDHs) are key regulators of flux through biosynthetic and oxidative pathways in response to cellular energy levels. Here we present the first structures of a eukaryotic member of this enzyme family, the allosteric, hetero-octameric, NAD(+)-specific IDH from yeast in three forms: 1) without ligands, 2) with bound analog citrate, and 3) with bound citrate + AMP. The structures reveal the molecular basis for ligand binding to homologous but distinct regulatory and catalytic sites positioned at the interfaces between IDH1 and IDH2 subunits and define pathways of communication between heterodimers and heterotetramers in the hetero-octamer. Disulfide bonds observed at the heterotetrameric interfaces in the unliganded IDH hetero-octamer are reduced in the ligand-bound forms, suggesting a redox regulatory mechanism that may be analogous to the "on-off" regulation of non-allosteric bacterial IDHs via phosphorylation. The results strongly suggest that eukaryotic IDH enzymes are exquisitely tuned to ensure that allosteric activation occurs only when concentrations of isocitrate are elevated.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-BLV is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLV OCA].
+</div>
+<div class="pdbe-citations 3blv" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Allosteric motions in structures of yeast NAD+-specific isocitrate dehydrogenase., Taylor AB, Hu G, Hart PJ, McAlister-Henn L, J Biol Chem. 2008 Apr 18;283(16):10872-80. Epub 2008 Feb 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18256028 18256028]
+*[[Isocitrate dehydrogenase 3D structures|Isocitrate dehydrogenase 3D structures]]
-[[Category: Protein complex]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Hart, P J.]]
+[[Category: Hart PJ]]
-[[Category: Hu, G.]]
+[[Category: Hu G]]
-[[Category: McAlister-Henn, L.]]
+[[Category: McAlister-Henn L]]
-[[Category: Taylor, A B.]]
+[[Category: Taylor AB]]
-[[Category: Allosteric enzyme]]
-[[Category: Allostery]]
-[[Category: Decarboxylase]]
-[[Category: Dehydrogenase]]
-[[Category: Magnesium]]
-[[Category: Manganese]]
-[[Category: Metal-binding]]
-[[Category: Mitochondrion]]
-[[Category: Nad]]
-[[Category: Oxidative metabolism]]
-[[Category: Oxidoreductase]]
-[[Category: Phosphoprotein]]
-[[Category: Rna-binding]]
-[[Category: Tca cycle]]
-[[Category: Transit peptide]]
-[[Category: Tricarboxylic acid cycle]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 14 11:40:39 2008''