1grp: Difference between revisions

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'''REGULATORY AND CATALYTIC MECHANISMS IN ESCHERICHIA COLI ISOCITRATE DEHYDROGENASE: MULTIPLE ROLES FOR N115'''<br />


==Overview==
==REGULATORY AND CATALYTIC MECHANISMS IN ESCHERICHIA COLI ISOCITRATE DEHYDROGENASE: MULTIPLE ROLES FOR N115==
Inactivation of Escherichia coli isocitrate dehydrogenase upon, phosphorylation at S113 depends upon the direct electrostatic repulsion of, the negatively charged gamma-carboxylate of isocitrate by the negatively, charged phosphoserine. The effect is mimicked by replacing S113 with, aspartate or glutamate, which reduce performance (kcat/K(i).isocitrat/, Km.NADP) by a factor of 10(7). Here, we demonstrate that the inactivating, effects of the electrostatic repulsion are completely eliminated by a, second-site mutation, and provide the structural basis for this striking, example of intragenic suppression. N115 is adjacent to S113 on one face of, the D-helix, interacts with isocitrate and NADP+, and has been postulated, to serve in both substrate binding and in catalysis. The single N115L, substitution reduces affinity for isocitrate by a factor of 50 and, performance by a factor of 500. However, the N115L substitution completely, suppresses the inactivating electrostatic effects of S113D or S113E: the, performance of the double mutants is 10(5) higher than the S113D and S113E, single mutants. These mutations have little effect on the kinetics of, alternative substrates, which lack the charged gamma-carboxylate of, isocitrate. Both glutamate and aspartate at site 113 remain fully ionized, in the presence of leucine. In the crystal structure of the N115L mutant, the leucine adopts a different conformer from the wild-type asparagine., Repacking around the leucine forces the amino-terminus of the D-helix away, from the rest of the active site. The hydrogen bond between E113 and N115, in the S113E single mutant is broken in the S113E/N115L mutant, allowing, the glutamate side chain to move away from the gamma-carboxylate of, isocitrate. These movements increase the distance between the, carboxylates, diminish the electrostatic repulsion, and lead to the, remarkably high activity of the S113E/N115L mutant.
<StructureSection load='1grp' size='340' side='right'caption='[[1grp]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1grp]] 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=1GRP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GRP 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]] 2.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ICT:ISOCITRIC+ACID'>ICT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1grp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1grp OCA], [https://pdbe.org/1grp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1grp RCSB], [https://www.ebi.ac.uk/pdbsum/1grp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1grp 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/gr/1grp_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=1grp ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1GRP 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 MG and ICT 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=1GRP OCA].
*[[Isocitrate dehydrogenase 3D structures|Isocitrate dehydrogenase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Second-site suppression of regulatory phosphorylation in Escherichia coli isocitrate dehydrogenase., Chen R, Grobler JA, Hurley JH, Dean AM, Protein Sci. 1996 Feb;5(2):287-95. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8745407 8745407]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Isocitrate dehydrogenase (NADP(+))]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Grobler JA]]
[[Category: Grobler, J.A.]]
[[Category: Hurley JH]]
[[Category: Hurley, J.H.]]
[[Category: ICT]]
[[Category: MG]]
[[Category: glyoxylate bypass]]
[[Category: nadp]]
[[Category: oxidoreductase]]
[[Category: phosphorylation]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 16:15:20 2007''

Latest revision as of 10:26, 7 February 2024

REGULATORY AND CATALYTIC MECHANISMS IN ESCHERICHIA COLI ISOCITRATE DEHYDROGENASE: MULTIPLE ROLES FOR N115REGULATORY AND CATALYTIC MECHANISMS IN ESCHERICHIA COLI ISOCITRATE DEHYDROGENASE: MULTIPLE ROLES FOR N115

Structural highlights

1grp is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
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

1grp, resolution 2.50Å

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OCA
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