2ji3: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2ji3.jpg|left|200px]]
- {{Structure
+==X-ray structure of the iron-peroxide intermediate of superoxide reductase (E114A mutant) from Desulfoarculus baarsii==
-|PDB= 2ji3 |SIZE=350|CAPTION= <scene name='initialview01'>2ji3</scene>, resolution 1.95&Aring;
+<StructureSection load='2ji3' size='340' side='right'caption='[[2ji3]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:Per+Binding+Site+For+Chain+D'>AC1</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene> and <scene name='pdbligand=PER:PEROXIDE ION'>PER</scene>
+<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>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Superoxide_reductase Superoxide reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.2 1.15.1.2]
+</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>
-|GENE=
+<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>
-}}
+<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>
+<div class="pdbe-citations 2ji3" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-JI3 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_baarsii Desulfovibrio baarsii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JI3 OCA].
+*[[Superoxide Reductase|Superoxide Reductase]]
-[[Category: Desulfovibrio baarsii]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Superoxide reductase]]
+__TOC__
-[[Category: Adam, V.]]
+</StructureSection>
-[[Category: Amara, P.]]
+[[Category: Desulfarculus baarsii]]
-[[Category: Bourgeois, D.]]
+[[Category: Large Structures]]
-[[Category: Carpentier, P.]]
+[[Category: Adam V]]
-[[Category: Katona, G.]]
+[[Category: Amara P]]
-[[Category: Niviere, V.]]
+[[Category: Bourgeois D]]
-[[Category: Ohana, J.]]
+[[Category: Carpentier P]]
-[[Category: Tsanov, N.]]
+[[Category: Katona G]]
-[[Category: CA]]
+[[Category: Niviere V]]
-[[Category: FE]]
+[[Category: Ohana J]]
-[[Category: NO3]]
+[[Category: Tsanov N]]
-[[Category: PER]]
-[[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]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:42:13 2008''