1pb3: Difference between revisions

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New page: left|200px<br /><applet load="1pb3" size="450" color="white" frame="true" align="right" spinBox="true" caption="1pb3, resolution 1.70Å" /> '''Sites of binding and...
 
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[[Image:1pb3.jpg|left|200px]]<br /><applet load="1pb3" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1pb3, resolution 1.70&Aring;" />
'''Sites of binding and orientation in a four location model for protein stereospecificity.'''<br />


==Overview==
==Sites of binding and orientation in a four location model for protein stereospecificity.==
The stereospecificity of the enzyme isocitrate dehydrogenase was examined, by steady-state kinetics and x-ray crystallography. The enzyme has the, intriguing property that the apoenzyme in the absence of divalent metal, showed a selectivity for the inactive l-enantiomer of the substrate, isocitrate, whereas the enzyme containing magnesium showed selectivity for, the physiologically active d-enantiomer. The hydrogen atom on the C2, carbon that is transferred during the reaction was, in both the d- and, l-isocitrate complexes, in an orientation very close to that expected for, delivery of a hydride ion to the cosubstrate NADP+. The beta-carboxylate, that is eliminated as a CO2 molecule during the reaction occupied the same, site on the protein in both the d- and l-isocitrate complexes. In, addition, the C3 carbon was in the same protein site in both the d- and, l-enantiomers. Only the fourth group, the OH atom, was in a very different, position in the apo enzyme and in the metal-containing complexes. A, four-location model is necessary to explain the enantiomeric specificity, of IDH in contrast to the conventional three-point attachment model. The, thermodynamic and kinetic ramifications of this model are explored.
<StructureSection load='1pb3' size='340' side='right'caption='[[1pb3]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1pb3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PB3 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]] 1.7&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1pb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pb3 OCA], [https://pdbe.org/1pb3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pb3 RCSB], [https://www.ebi.ac.uk/pdbsum/1pb3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pb3 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/pb/1pb3_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=1pb3 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1PB3 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 SO4 and GOL 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=1PB3 OCA].
*[[Isocitrate dehydrogenase 3D structures|Isocitrate dehydrogenase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Sites of binding and orientation in a four-location model for protein stereospecificity., Mesecar AD, Koshland DE Jr, IUBMB Life. 2000 May;49(5):457-66. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10902579 10902579]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Isocitrate dehydrogenase (NADP(+))]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Koshland Jr DE]]
[[Category: Jr., D.E.Koshland.]]
[[Category: Mesecar AD]]
[[Category: Mesecar, A.D.]]
[[Category: GOL]]
[[Category: SO4]]
[[Category: entantiomer]]
[[Category: idh]]
[[Category: isocitrate dehydrogense]]
[[Category: stereospecificity]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:39:10 2007''

Latest revision as of 08:06, 14 February 2024

Sites of binding and orientation in a four location model for protein stereospecificity.

1pb3, resolution 1.70Å

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