2ji3: Difference between revisions

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-[[Image:2ji3.png|left|200px]]
-<!--
+==X-ray structure of the iron-peroxide intermediate of superoxide reductase (E114A mutant) from Desulfoarculus baarsii==
-The line below this paragraph, containing "STRUCTURE_2ji3", creates the "Structure Box" on the page.
+<StructureSection load='2ji3' size='340' side='right'caption='[[2ji3]], [[Resolution|resolution]] 1.95&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'>[[2ji3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfarculus_baarsii Desulfarculus baarsii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JI3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JI3 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]] 1.95&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene></td></tr>
-{{STRUCTURE_2ji3|  PDB=2ji3  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ji3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ji3 OCA], [https://pdbe.org/2ji3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ji3 RCSB], [https://www.ebi.ac.uk/pdbsum/2ji3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ji3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DFX_DESB2 DFX_DESB2] Catalyzes the one-electron reduction of superoxide anion radical to hydrogen peroxide at a nonheme ferrous iron center. Plays a fundamental role in case of oxidative stress via its superoxide detoxification activity.<ref>PMID:10617593</ref>
+== 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/ji/2ji3_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=2ji3 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Iron-peroxide intermediates are central in the reaction cycle of many iron-containing biomolecules. We trapped iron(III)-(hydro)peroxo species in crystals of superoxide reductase (SOR), a nonheme mononuclear iron enzyme that scavenges superoxide radicals. X-ray diffraction data at 1.95 angstrom resolution and Raman spectra recorded in crystallo revealed iron-(hydro)peroxo intermediates with the (hydro)peroxo group bound end-on. The dynamic SOR active site promotes the formation of transient hydrogen bond networks, which presumably assist the cleavage of the iron-oxygen bond in order to release the reaction product, hydrogen peroxide.
-===X-RAY STRUCTURE OF THE IRON-PEROXIDE INTERMEDIATE OF SUPEROXIDE REDUCTASE (E114A MUTANT) FROM DESULFOARCULUS BAARSII===
+Raman-assisted crystallography reveals end-on peroxide intermediates in a nonheme iron enzyme.,Katona G, Carpentier P, Niviere V, Amara P, Adam V, Ohana J, Tsanov N, Bourgeois D Science. 2007 Apr 20;316(5823):449-53. PMID:17446401<ref>PMID:17446401</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_17446401}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2ji3" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17446401 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_17446401}}
-==About this Structure==
-[[2ji3]] is a 4 chain structure of [[Superoxide Reductase]] with sequence from [http://en.wikipedia.org/wiki/Desulfarculus_baarsii Desulfarculus baarsii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JI3 OCA].
 ==See Also==
-*[[Superoxide Reductase]]
+*[[Superoxide Reductase|Superoxide Reductase]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:17446401</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Desulfarculus baarsii]]
-[[Category: Superoxide reductase]]
+[[Category: Large Structures]]
-[[Category: Adam, V.]]
+[[Category: Adam V]]
-[[Category: Amara, P.]]
+[[Category: Amara P]]
-[[Category: Bourgeois, D.]]
+[[Category: Bourgeois D]]
-[[Category: Carpentier, P.]]
+[[Category: Carpentier P]]
-[[Category: Katona, G.]]
+[[Category: Katona G]]
-[[Category: Niviere, V.]]
+[[Category: Niviere V]]
-[[Category: Ohana, J.]]
+[[Category: Ohana J]]
-[[Category: Tsanov, N.]]
+[[Category: Tsanov N]]
-[[Category: Detoxification]]
-[[Category: Electron transport]]
-[[Category: Intermediate trapping]]
-[[Category: Iron]]
-[[Category: Metal-binding]]
-[[Category: Microspectrophotometry]]
-[[Category: Oxidoreductase]]
-[[Category: Raman spectroscopy]]
-[[Category: Redox state]]
-[[Category: Superoxide reductase]]
-[[Category: Transport]]