View source for 2nvl


==Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (sulfonic acid form)==
<StructureSection load='2nvl' size='340' side='right'caption='[[2nvl]], [[Resolution|resolution]] 2.36&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2nvl]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix_K1 Aeropyrum pernix K1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NVL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NVL 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]] 2.36&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</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=2nvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nvl OCA], [https://pdbe.org/2nvl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nvl RCSB], [https://www.ebi.ac.uk/pdbsum/2nvl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nvl ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/TDXH_AERPE TDXH_AERPE] 
== 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/nv/2nvl_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=2nvl ConSurf].
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== Publication Abstract from PubMed ==
The oxidation of thiol groups in proteins is a common event in biochemical processes involving disulfide bond formation and in response to an increased level of reactive oxygen species. It has been widely accepted that the oxidation of a cysteine side chain is initiated by the formation of cysteine sulfenic acid (Cys-SOH). Here, we demonstrate a mechanism of thiol oxidation through a hypervalent sulfur intermediate by presenting crystallographic evidence from an archaeal peroxiredoxin (Prx), the thioredoxin peroxidase from Aeropyrum pernix K1 (ApTPx). The reaction of Prx, which is the reduction of a peroxide, depends on the redox active cysteine side chains. Oxidation by hydrogen peroxide converted the active site peroxidatic Cys-50 of ApTPx to a cysteine sulfenic acid derivative, followed by further oxidation to cysteine sulfinic and sulfonic acids. The crystal structure of the cysteine sulfenic acid derivative was refined to 1.77 A resolution with R(cryst) and R(free) values of 18.8% and 22.0%, respectively. The refined structure, together with quantum chemical calculations, revealed that the sulfenic acid derivative is a type of sulfurane, a hypervalent sulfur compound, and that the S(gamma) atom is covalently linked to the N(delta1) atom of the neighboring His-42. The reaction mechanism is revealed by the hydrogen bond network around the peroxidatic cysteine and the motion of the flexible loop covering the active site and by quantum chemical calculations. This study provides evidence that a hypervalent sulfur compound occupies an important position in biochemical processes.

Oxidation of archaeal peroxiredoxin involves a hypervalent sulfur intermediate.,Nakamura T, Yamamoto T, Abe M, Matsumura H, Hagihara Y, Goto T, Yamaguchi T, Inoue T Proc Natl Acad Sci U S A. 2008 Apr 29;105(17):6238-42. Epub 2008 Apr 24. PMID:18436649<ref>PMID:18436649</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 2nvl" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Aeropyrum pernix K1]]
[[Category: Large Structures]]
[[Category: Abe M]]
[[Category: Goto T]]
[[Category: Hagihara Y]]
[[Category: Inoue T]]
[[Category: Matsumura H]]
[[Category: Nakamura T]]
[[Category: Yamaguchi T]]
[[Category: Yamamoto T]]