3blw

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[[Image:3blw.jpg|left|200px]]
 
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{{Structure
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==Yeast Isocitrate Dehydrogenase with Citrate and AMP Bound in the Regulatory Subunits==
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|PDB= 3blw |SIZE=350|CAPTION= <scene name='initialview01'>3blw</scene>, resolution 4.3&Aring;
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<StructureSection load='3blw' size='340' side='right'caption='[[3blw]], [[Resolution|resolution]] 4.30&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Flc+Binding+Site+For+Residue+A+1001'>AC1</scene>, <scene name='pdbsite=AC2:Flc+Binding+Site+For+Residue+C+1002'>AC2</scene>, <scene name='pdbsite=AC3:Flc+Binding+Site+For+Residue+E+1003'>AC3</scene>, <scene name='pdbsite=AC4:Flc+Binding+Site+For+Residue+G+1004'>AC4</scene>, <scene name='pdbsite=AC5:Flc+Binding+Site+For+Residue+I+1005'>AC5</scene>, <scene name='pdbsite=AC6:Flc+Binding+Site+For+Residue+K+1006'>AC6</scene>, <scene name='pdbsite=AC7:Flc+Binding+Site+For+Residue+M+1007'>AC7</scene>, <scene name='pdbsite=AC8:Flc+Binding+Site+For+Residue+O+1008'>AC8</scene>, <scene name='pdbsite=AC9:Amp+Binding+Site+For+Residue+A+2001'>AC9</scene>, <scene name='pdbsite=BC1:Amp+Binding+Site+For+Residue+C+2002'>BC1</scene>, <scene name='pdbsite=BC2:Amp+Binding+Site+For+Residue+E+2003'>BC2</scene>, <scene name='pdbsite=BC3:Amp+Binding+Site+For+Residue+G+2004'>BC3</scene>, <scene name='pdbsite=BC4:Amp+Binding+Site+For+Residue+I+2005'>BC4</scene>, <scene name='pdbsite=BC5:Amp+Binding+Site+For+Residue+K+2006'>BC5</scene>, <scene name='pdbsite=BC6:Amp+Binding+Site+For+Residue+M+2007'>BC6</scene> and <scene name='pdbsite=BC7:Amp+Binding+Site+For+Residue+O+2008'>BC7</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>
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<table><tr><td colspan='2'>[[3blw]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. The September 2010 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Isocitrate Dehydrogenase'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2010_9 10.2210/rcsb_pdb/mom_2010_9]. The October 2012 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Citric Acid Cycle'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2012_10 10.2210/rcsb_pdb/mom_2012_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BLW FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase_(NAD(+)) Isocitrate dehydrogenase (NAD(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.41 1.1.1.41] </span>
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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]] 4.3&#8491;</td></tr>
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|GENE= IDH1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), IDH2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene></td></tr>
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|DOMAIN=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3blw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blw OCA], [https://pdbe.org/3blw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3blw RCSB], [https://www.ebi.ac.uk/pdbsum/3blw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3blw ProSAT]</span></td></tr>
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|RELATEDENTRY=[[3blx|3BLX]], [[3blv|3BLV]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3blw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blw OCA], [http://www.ebi.ac.uk/pdbsum/3blw PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3blw RCSB]</span>
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== Function ==
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}}
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[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bl/3blw_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3blw ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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'''Yeast Isocitrate Dehydrogenase with Citrate and AMP Bound in the Regulatory Subunits'''
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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>
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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 3blw" style="background-color:#fffaf0;"></div>
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==About this Structure==
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==See Also==
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3BLW 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=3BLW OCA].
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*[[Isocitrate dehydrogenase 3D structures|Isocitrate dehydrogenase 3D structures]]
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[[Category: Isocitrate dehydrogenase (NAD(+))]]
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== References ==
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[[Category: Protein complex]]
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Citric Acid Cycle]]
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[[Category: Isocitrate Dehydrogenase]]
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[[Category: Large Structures]]
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[[Category: RCSB PDB Molecule of the Month]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Hart, P J.]]
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[[Category: Hart PJ]]
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[[Category: Hu, G.]]
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[[Category: Hu G]]
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[[Category: McAlister-Henn, L.]]
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[[Category: McAlister-Henn L]]
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[[Category: Taylor, A B.]]
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[[Category: Taylor AB]]
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[[Category: allosteric enzyme]]
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[[Category: allostery]]
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[[Category: decarboxylase]]
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[[Category: dehydrogenase]]
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[[Category: magnesium]]
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[[Category: manganese]]
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[[Category: metal-binding]]
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[[Category: mitochondrion]]
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[[Category: nad]]
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[[Category: oxidative metabolism]]
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[[Category: oxidoreductase]]
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[[Category: phosphoprotein]]
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[[Category: rna-binding]]
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[[Category: tca cycle]]
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[[Category: transit peptide]]
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[[Category: tricarboxylic acid cycle]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:27:26 2008''
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Current revision

Yeast Isocitrate Dehydrogenase with Citrate and AMP Bound in the Regulatory Subunits

PDB ID 3blw

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