9icd

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(New page: 200px<br /><applet load="9icd" size="450" color="white" frame="true" align="right" spinBox="true" caption="9icd, resolution 2.5&Aring;" /> '''CATALYTIC MECHANISM O...)
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[[Image:9icd.gif|left|200px]]<br /><applet load="9icd" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="9icd, resolution 2.5&Aring;" />
 
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'''CATALYTIC MECHANISM OF NADP+-DEPENDENT ISOCITRATE DEHYDROGENASE: IMPLICATIONS FROM THE STRUCTURES OF MAGNESIUM-ISOCITRATE AND NADP+ COMPLEXES'''<br />
 
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==Overview==
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==CATALYTIC MECHANISM OF NADP+-DEPENDENT ISOCITRATE DEHYDROGENASE: IMPLICATIONS FROM THE STRUCTURES OF MAGNESIUM-ISOCITRATE AND NADP+ COMPLEXES==
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The structures of NADP+ and magnesium isocitrate bound to the, NADP(+)-dependent isocitrate dehydrogenase of Escherichia coli have been, determined and refined at 2.5-A resolution. NADP+ is bound by the large, domain of isocitrate dehydrogenase, a structure that has little similarity, to the supersecondary structure of the nucleotide-binding domain of the, lactate dehydrogenase-like family of nucleotide-binding proteins. The, coenzyme-binding site confirms the fundamentally different evolution of, the isocitrate dehydrogenase-like and the lactate dehydrogenase-like, classes of nucleotide-binding proteins. In the magnesium-isocitrate, complex, magnesium is coordinated to the alpha-carboxylate and, alpha-hydroxyl oxygen of isocitrate in a manner suitable for stabilization, of a negative charge on the hydroxyl oxygen during both the, dehydrogenation and decarboxylation steps of the conversion of isocitrate, to alpha-ketoglutarate. The metal ion is also coordinated by aspartate, side chains 283' (of the second subunit of the dimer) and 307 and two, water molecules in a roughly octahedral arrangement. On the basis of the, geometry of the active site, the base functioning in the dehydrogenation, step is most likely aspartate 283'. E. coli isocitrate dehydrogenase, transfers a hydride stereospecifically to the A-side of NADP+, and models, for a reactive ternary complex consistent with this stereospecificity are, discussed.
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<StructureSection load='9icd' size='340' side='right'caption='[[9icd]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[9icd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. 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=9ICD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9ICD FirstGlance]. <br>
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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]] 2.5&#8491;</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=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
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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=9icd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9icd OCA], [https://pdbe.org/9icd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9icd RCSB], [https://www.ebi.ac.uk/pdbsum/9icd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9icd ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/IDH_ECOLI IDH_ECOLI]
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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/ic/9icd_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=9icd ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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9ICD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with NAP as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase_(NADP(+)) Isocitrate dehydrogenase (NADP(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.42 1.1.1.42] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=9ICD OCA].
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*[[Isocitrate dehydrogenase 3D structures|Isocitrate dehydrogenase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Catalytic mechanism of NADP(+)-dependent isocitrate dehydrogenase: implications from the structures of magnesium-isocitrate and NADP+ complexes., Hurley JH, Dean AM, Koshland DE Jr, Stroud RM, Biochemistry. 1991 Sep 3;30(35):8671-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1888729 1888729]
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[[Category: Citric Acid Cycle]]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Isocitrate dehydrogenase (NADP(+))]]
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[[Category: Isocitrate Dehydrogenase]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Dean, A.M.]]
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[[Category: RCSB PDB Molecule of the Month]]
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[[Category: Hurley, J.H.]]
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[[Category: Dean AM]]
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[[Category: Koshlandjunior, D.E.]]
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[[Category: Hurley JH]]
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[[Category: Stroud, R.M.]]
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[[Category: Koshland Jr DE]]
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[[Category: NAP]]
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[[Category: Stroud RM]]
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[[Category: oxidoreductase (nad(a)-choh(d))]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:03:07 2007''
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Current revision

CATALYTIC MECHANISM OF NADP+-DEPENDENT ISOCITRATE DEHYDROGENASE: IMPLICATIONS FROM THE STRUCTURES OF MAGNESIUM-ISOCITRATE AND NADP+ COMPLEXES

PDB ID 9icd

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