3blv: Difference between revisions

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-[[Image:3blv.jpg|left|200px]]
-<!--
+==Yeast Isocitrate Dehydrogenase with Citrate Bound in the Regulatory Subunits==
-The line below this paragraph, containing "STRUCTURE_3blv", creates the "Structure Box" on the page.
+<StructureSection load='3blv' size='340' side='right'caption='[[3blv]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</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>
-{{STRUCTURE_3blv|  PDB=3blv  |  SCENE=  }}
+<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.
-'''Yeast Isocitrate Dehydrogenase with Citrate Bound in the Regulatory Subunits'''
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3blv" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-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].
+*[[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 Sun May  4 20:54:29 2008''