1ika

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[[Image:1ika.gif|left|200px]]
 
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{{Structure
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==STRUCTURE OF ISOCITRATE DEHYDROGENASE WITH ALPHA-KETOGLUTARATE AT 2.7 ANGSTROMS RESOLUTION: CONFORMATIONAL CHANGES INDUCED BY DECARBOXYLATION OF ISOCITRATE==
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|PDB= 1ika |SIZE=350|CAPTION= <scene name='initialview01'>1ika</scene>, resolution 2.7&Aring;
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<StructureSection load='1ika' size='340' side='right'caption='[[1ika]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> and <scene name='pdbligand=AKG:2-OXYGLUTARIC ACID'>AKG</scene>
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<table><tr><td colspan='2'>[[1ika]] 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]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IKA FirstGlance]. <br>
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|ACTIVITY= [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]
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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]] 2.7&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
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}}
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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=1ika FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ika OCA], [https://pdbe.org/1ika PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ika RCSB], [https://www.ebi.ac.uk/pdbsum/1ika PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ika 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/ik/1ika_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=1ika ConSurf].
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<div style="clear:both"></div>
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'''STRUCTURE OF ISOCITRATE DEHYDROGENASE WITH ALPHA-KETOGLUTARATE AT 2.7 ANGSTROMS RESOLUTION: CONFORMATIONAL CHANGES INDUCED BY DECARBOXYLATION OF ISOCITRATE'''
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==See Also==
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*[[Isocitrate dehydrogenase 3D structures|Isocitrate dehydrogenase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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The structure of the isocitrate dehydrogenase (IDH) complex with bound alpha-ketoglutarate, Ca2+, and NADPH was solved at 2.7-A resolution. The alpha-ketoglutarate binds in the active site at the same position and orientation as isocitrate, with a difference between the two bound molecules of about 0.8 A. The Ca2+ metal is coordinated by alpha-ketoglutarate, three conserved aspartate residues, and a pair of water molecules. The largest motion in the active site relative to the isocitrate enzyme complex is observed for tyrosine 160, which originally forms a hydrogen bond to the labile carboxyl group of isocitrate and moves to form a new hydrogen bond to Asp 307 in the complex with alpha-ketoglutarate. This triggers a number of significant movements among several short loops and adjoining secondary structural elements in the enzyme, most of which participate in dimer stabilization and formation of the active-site cleft. These rearrangements are similar to the ligand-binding-induced movements observed in globins and insulin and serve as a model for an enzymatic mechanism which involves local shifts of secondary structural elements during turnover, rather than large-scale domain closures or loop transitions induced by substrate binding such as those observed in hexokinase or triosephosphate isomerase.
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==About this Structure==
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1IKA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IKA OCA].
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==Reference==
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Structure of isocitrate dehydrogenase with alpha-ketoglutarate at 2.7-A resolution: conformational changes induced by decarboxylation of isocitrate., Stoddard BL, Koshland DE Jr, Biochemistry. 1993 Sep 14;32(36):9317-22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8369301 8369301]
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[[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: Junior, D E.Koshland.]]
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[[Category: RCSB PDB Molecule of the Month]]
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[[Category: Stoddard, B L.]]
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[[Category: Koshland Junior DE]]
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[[Category: AKG]]
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[[Category: Stoddard BL]]
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[[Category: CA]]
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[[Category: oxidoreductase(nad(a)-choh(d))]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 11:51:26 2008''
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Current revision

STRUCTURE OF ISOCITRATE DEHYDROGENASE WITH ALPHA-KETOGLUTARATE AT 2.7 ANGSTROMS RESOLUTION: CONFORMATIONAL CHANGES INDUCED BY DECARBOXYLATION OF ISOCITRATE

PDB ID 1ika

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