2h70: Difference between revisions
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==Crystal Structure of Thioredoxin Mutant D9E in Hexagonal (p61) Space Group== | |||
<StructureSection load='2h70' size='340' side='right'caption='[[2h70]], [[Resolution|resolution]] 2.70Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2h70]] is a 2 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=2H70 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H70 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]] 2.7Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=2h70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h70 OCA], [https://pdbe.org/2h70 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h70 RCSB], [https://www.ebi.ac.uk/pdbsum/2h70 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h70 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/THIO_ECOLI THIO_ECOLI] Participates in various redox reactions through the reversible oxidation of its active center dithiol to a disulfide and catalyzes dithiol-disulfide exchange reactions. | |||
== 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/h7/2h70_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=2h70 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
We have determined the effect of mutations involving isoleucine and valine (i.e., mutations I-->V and V-->I) on the stability of Escherichia coli thioredoxin. Despite the similarity in chemical structure (V and I differ only in a methyl group), we find that many environments are optimized to a significant extent for either V or I. We find, furthermore, that a plot of effect of hydrophobic mutations on stability versus packing density shows a strikingly simple pattern that clearly reflects evolutionary structural optimization. The existence of such patterns suggests the possibility of rationalizing (and perhaps even predicting) mutation effects on protein stability on the basis of evolutionary models. By "evolutionary model" we specifically refer in this context to a model for mutation effects on stability in which certain physical features of the mutated residue environments are evaluated from an assumption regarding how such environments have been selected during protein evolution (as opposed to a purely "physical model" in which those features would be derived from some kind of energetics analysis of the protein structural characteristics). To illustrate this novel approach and provide general guidelines for its application, we develop here a simple evolutionary model that successfully explains the effect of the I<-->V mutations on thioredoxin stability. | |||
A stability pattern of protein hydrophobic mutations that reflects evolutionary structural optimization.,Godoy-Ruiz R, Perez-Jimenez R, Ibarra-Molero B, Sanchez-Ruiz JM Biophys J. 2005 Nov;89(5):3320-31. Epub 2005 Aug 12. PMID:16100262<ref>PMID:16100262</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2h70" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Thioredoxin|Thioredoxin]] | *[[Thioredoxin 3D structures|Thioredoxin 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Gavira | [[Category: Large Structures]] | ||
[[Category: Godoy-Ruiz | [[Category: Gavira JA]] | ||
[[Category: Ibarra-Molero | [[Category: Godoy-Ruiz R]] | ||
[[Category: Sanchez-Ruiz | [[Category: Ibarra-Molero B]] | ||
[[Category: Sanchez-Ruiz JM]] | |||
Latest revision as of 12:53, 30 August 2023
Crystal Structure of Thioredoxin Mutant D9E in Hexagonal (p61) Space GroupCrystal Structure of Thioredoxin Mutant D9E in Hexagonal (p61) Space Group
Structural highlights
FunctionTHIO_ECOLI Participates in various redox reactions through the reversible oxidation of its active center dithiol to a disulfide and catalyzes dithiol-disulfide exchange reactions. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedWe have determined the effect of mutations involving isoleucine and valine (i.e., mutations I-->V and V-->I) on the stability of Escherichia coli thioredoxin. Despite the similarity in chemical structure (V and I differ only in a methyl group), we find that many environments are optimized to a significant extent for either V or I. We find, furthermore, that a plot of effect of hydrophobic mutations on stability versus packing density shows a strikingly simple pattern that clearly reflects evolutionary structural optimization. The existence of such patterns suggests the possibility of rationalizing (and perhaps even predicting) mutation effects on protein stability on the basis of evolutionary models. By "evolutionary model" we specifically refer in this context to a model for mutation effects on stability in which certain physical features of the mutated residue environments are evaluated from an assumption regarding how such environments have been selected during protein evolution (as opposed to a purely "physical model" in which those features would be derived from some kind of energetics analysis of the protein structural characteristics). To illustrate this novel approach and provide general guidelines for its application, we develop here a simple evolutionary model that successfully explains the effect of the I<-->V mutations on thioredoxin stability. A stability pattern of protein hydrophobic mutations that reflects evolutionary structural optimization.,Godoy-Ruiz R, Perez-Jimenez R, Ibarra-Molero B, Sanchez-Ruiz JM Biophys J. 2005 Nov;89(5):3320-31. Epub 2005 Aug 12. PMID:16100262[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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