1ika: Difference between revisions

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New page: left|200px<br /><applet load="1ika" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ika, resolution 2.7Å" /> '''STRUCTURE OF ISOCITRA...
 
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[[Image:1ika.gif|left|200px]]<br /><applet load="1ika" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1ika, resolution 2.7&Aring;" />
'''STRUCTURE OF ISOCITRATE DEHYDROGENASE WITH ALPHA-KETOGLUTARATE AT 2.7 ANGSTROMS RESOLUTION: CONFORMATIONAL CHANGES INDUCED BY DECARBOXYLATION OF ISOCITRATE'''<br />


==Overview==
==STRUCTURE OF ISOCITRATE DEHYDROGENASE WITH ALPHA-KETOGLUTARATE AT 2.7 ANGSTROMS RESOLUTION: CONFORMATIONAL CHANGES INDUCED BY DECARBOXYLATION OF ISOCITRATE==
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.
<StructureSection load='1ika' size='340' side='right'caption='[[1ika]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
<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>
</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>
<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>
<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>
</table>
== Function ==
[https://www.uniprot.org/uniprot/IDH_ECOLI IDH_ECOLI]
== 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/ik/1ika_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1ika ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1IKA 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 CA and AKG as [http://en.wikipedia.org/wiki/ligands ligands]. 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=1IKA OCA].
*[[Isocitrate dehydrogenase 3D structures|Isocitrate dehydrogenase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=8369301 8369301]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Isocitrate dehydrogenase (NADP(+))]]
[[Category: Isocitrate Dehydrogenase]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Junior, D.E.Koshland.]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Stoddard, B.L.]]
[[Category: Koshland Junior DE]]
[[Category: AKG]]
[[Category: Stoddard BL]]
[[Category: CA]]
[[Category: oxidoreductase(nad(a)-choh(d))]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 17:28:00 2007''

Latest revision as of 10:36, 7 February 2024

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

Structural highlights

1ika is a 1 chain structure with sequence from Escherichia coli. The September 2010 RCSB PDB Molecule of the Month feature on Isocitrate Dehydrogenase by David Goodsell is 10.2210/rcsb_pdb/mom_2010_9. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.7Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IDH_ECOLI

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1ika, resolution 2.70Å

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