2vl3: Difference between revisions

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-{{Seed}}
-[[Image:2vl3.jpg|left|200px]]
-<!--
+==Oxidized and reduced forms of human peroxiredoxin 5==
-The line below this paragraph, containing "STRUCTURE_2vl3", creates the "Structure Box" on the page.
+<StructureSection load='2vl3' size='340' side='right'caption='[[2vl3]], [[Resolution|resolution]] 1.83&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'>[[2vl3]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VL3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VL3 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]] 1.83&#8491;</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=2vl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vl3 OCA], [https://pdbe.org/2vl3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vl3 RCSB], [https://www.ebi.ac.uk/pdbsum/2vl3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vl3 ProSAT]</span></td></tr>
-{{STRUCTURE_2vl3|  PDB=2vl3  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PRDX5_HUMAN PRDX5_HUMAN] Reduces hydrogen peroxide and alkyl hydroperoxides with reducing equivalents provided through the thioredoxin system. Involved in intracellular redox signaling.
+== 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/vl/2vl3_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=2vl3 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Peroxiredoxin 5 (PRDX5) belongs to the PRDX superfamily of thiol-dependent peroxidases able to reduce hydrogen peroxide, alkyl hydroperoxides and peroxynitrite. PRDX5 is classified in the atypical 2-Cys subfamily of PRDXs. In this subfamily, the oxidized form of the enzyme is characterized by the presence of an intramolecular disulfide bridge between the peroxidatic and the resolving cysteine residues. We report here three crystal forms in which this intramolecular disulfide bond is indeed observed. The structures are characterized by the expected local unfolding of the peroxidatic loop, but also by the unfolding of the resolving loop. A new type of interface between PRDX molecules is described. The three crystal forms were not oxidized in the same way and the influence of the oxidizing conditions is discussed.
-===OXIDIZED AND REDUCED FORMS OF HUMAN PEROXIREDOXIN 5===
+The crystal structures of oxidized forms of human peroxiredoxin 5 with an intramolecular disulfide bond confirm the proposed enzymatic mechanism for atypical 2-Cys peroxiredoxins.,Smeets A, Marchand C, Linard D, Knoops B, Declercq JP Arch Biochem Biophys. 2008 Sep 1;477(1):98-104. Epub 2008 May 4. PMID:18489898<ref>PMID:18489898</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2vl3" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18489898}}, adds the Publication Abstract to the page
+*[[Peroxiredoxin 3D structures|Peroxiredoxin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18489898 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18489898}}
+__TOC__
+</StructureSection>
-==About this Structure==
-VL3 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VL3 OCA].
-==Reference==
-The crystal structures of oxidized forms of human peroxiredoxin 5 with an intramolecular disulfide bond confirm the proposed enzymatic mechanism for atypical 2-Cys peroxiredoxins., Smeets A, Marchand C, Linard D, Knoops B, Declercq JP, Arch Biochem Biophys. 2008 Sep 1;477(1):98-104. Epub 2008 May 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18489898 18489898]
 [[Category: Homo sapiens]]
-[[Category: Peroxiredoxin]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Declercq JP]]
-[[Category: Declercq, J P.]]
+[[Category: Smeets A]]
-[[Category: Smeets, A.]]
-[[Category: Alternative initiation]]
-[[Category: Antioxidant]]
-[[Category: Antioxidant enzyme]]
-[[Category: Cytoplasm]]
-[[Category: Mitochondrion]]
-[[Category: Oxidoreductase]]
-[[Category: Peroxidase]]
-[[Category: Peroxiredoxin]]
-[[Category: Peroxisome]]
-[[Category: Polymorphism]]
-[[Category: Redox-active center]]
-[[Category: Thioredoxin fold]]
-[[Category: Thioredoxin peroxidase]]
-[[Category: Transit peptide]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 27 11:10:59 2008''