1yex: Difference between revisions

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-{{Seed}}
-[[Image:1yex.png|left|200px]]
-<!--
+==Structural and biochemical analysis of the link between enzymatic activity and oligomerization in AhpC, a bacterial peroxiredoxin.==
-The line below this paragraph, containing "STRUCTURE_1yex", creates the "Structure Box" on the page.
+<StructureSection load='1yex' size='340' side='right'caption='[[1yex]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1yex]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YEX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YEX FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1yex|  PDB=1yex  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yex OCA], [https://pdbe.org/1yex PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yex RCSB], [https://www.ebi.ac.uk/pdbsum/1yex PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yex ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AHPC_SALTY AHPC_SALTY] Directly reduces alkyl hydroperoxides with the use of electrons donated by the 57 kDa flavoprotein alkyl hydroperoxide reductase.
+== 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/ye/1yex_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1yex ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Peroxiredoxins (Prxs) make up a ubiquitous class (proposed EC 1.11.1.15) of cysteine-dependent peroxidases with roles in oxidant protection and signal transduction. An intriguing biophysical property of typical 2-Cys Prxs is the redox-dependent modulation of their oligomeric state between decamers and dimers at physiological concentrations. The functional consequences of this linkage are unknown, but on the basis of structural considerations, we hypothesized that decamer-building (dimer-dimer) interactions serve to stabilize a loop that forms the peroxidatic active site. Here, we address this important issue by studying mutations of Thr77 at the decamer-building interface of AhpC from Salmonella typhimurium. Ultracentrifugation studies revealed that two of the substitutions (T77I and T77D) successfully disrupted the decamer, while the third (T77V) actually enhanced decamer stability. Crystal structures of the decameric forms of all three mutant proteins provide a rationale for their properties. A new assay allowed the first ever measurement of the true k(cat) and K(m) values of wild-type AhpC with H(2)O(2), placing the catalytic efficiency at 4 x 10(7) M(-)(1) s(-)(1). T77V had slightly higher activity than wild-type enzyme, and both T77I and T77D exhibited ca. 100-fold lower catalytic efficiency, indicating that the decameric structure is quite important for, but not essential to, activity. The interplay between decamer formation and active site loop dynamics is emphasized by a decreased susceptibility of T77I and T77D to peroxide-mediated inactivation, and by an increase in the crystallographic B-factors in the active site loop, rather than at the site of the mutation, in the T77D variant.
-===Structural and biochemical analysis of the link between enzymatic activity and oligomerization in AhpC, a bacterial peroxiredoxin.===
+Analysis of the link between enzymatic activity and oligomeric state in AhpC, a bacterial peroxiredoxin.,Parsonage D, Youngblood DS, Sarma GN, Wood ZA, Karplus PA, Poole LB Biochemistry. 2005 Aug 9;44(31):10583-92. PMID:16060667<ref>PMID:16060667</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_16060667}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1yex" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16060667 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16060667}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-YEX is a 5 chains structure of sequences from [http://en.wikipedia.org/wiki/Salmonella_typhimurium Salmonella typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YEX OCA].
+[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
+[[Category: Karplus PA]]
-==Reference==
+[[Category: Parsonage D]]
-<ref group="xtra">PMID:16060667</ref><references group="xtra"/>
+[[Category: Poole LB]]
-[[Category: Salmonella typhimurium]]
+[[Category: Sarma GN]]
-[[Category: Karplus, P A.]]
+[[Category: Wood ZA]]
-[[Category: Parsonage, D.]]
+[[Category: Youngblood DS]]
-[[Category: Poole, L B.]]
-[[Category: Sarma, G N.]]
-[[Category: Wood, Z A.]]
-[[Category: Youngblood, D S.]]
-[[Category: Ahpc]]
-[[Category: Peroxidase]]
-[[Category: Peroxiredoxin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:23:09 2009''