1hd2: Difference between revisions

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-{{Seed}}
-[[Image:1hd2.png|left|200px]]
-<!--
+==Human peroxiredoxin 5==
-The line below this paragraph, containing "STRUCTURE_1hd2", creates the "Structure Box" on the page.
+<StructureSection load='1hd2' size='340' side='right'caption='[[1hd2]], [[Resolution|resolution]] 1.50&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'>[[1hd2]] is a 1 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=1HD2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HD2 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]] 1.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=BR:BROMIDE+ION'>BR</scene></td></tr>
-{{STRUCTURE_1hd2|  PDB=1hd2  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1hd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hd2 OCA], [https://pdbe.org/1hd2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hd2 RCSB], [https://www.ebi.ac.uk/pdbsum/1hd2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hd2 ProSAT]</span></td></tr>
+</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/hd/1hd2_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=1hd2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The peroxiredoxins define an emerging family of peroxidases able to reduce hydrogen peroxide and alkyl hydroperoxides with the use of reducing equivalents derived from thiol-containing donor molecules such as thioredoxin, glutathione, trypanothione and AhpF. Peroxiredoxins have been identified in prokaryotes as well as in eukaryotes. Peroxiredoxin 5 (PRDX5) is a novel type of mammalian thioredoxin peroxidase widely expressed in tissues and located cellularly to mitochondria, peroxisomes and cytosol. Functionally, PRDX5 has been implicated in antioxidant protective mechanisms as well as in signal transduction in cells. We report here the 1.5 A resolution crystal structure of human PRDX5 in its reduced form. The crystal structure reveals that PRDX5 presents a thioredoxin-like domain. Interestingly, the crystal structure shows also that PRDX5 does not form a dimer like other mammalian members of the peroxiredoxin family. In the reduced form of PRDX5, Cys47 and Cys151 are distant of 13.8 A although these two cysteine residues are thought to be involved in peroxide reductase activity by forming an intramolecular disulfide intermediate in the oxidized enzyme. These data suggest that the enzyme would necessitate a conformational change to form a disulfide bond between catalytic Cys47 and Cys151 upon oxidation according to proposed peroxide reduction mechanisms. Moreover, the presence of a benzoate ion, a hydroxyl radical scavenger, was noted close to the active-site pocket. The possible role of benzoate in the antioxidant activity of PRDX5 is discussed.
-===HUMAN PEROXIREDOXIN 5===
+Crystal structure of human peroxiredoxin 5, a novel type of mammalian peroxiredoxin at 1.5 A resolution.,Declercq JP, Evrard C, Clippe A, Stricht DV, Bernard A, Knoops B J Mol Biol. 2001 Aug 24;311(4):751-9. PMID:11518528<ref>PMID:11518528</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1hd2" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11518528}}, adds the Publication Abstract to the page
+*[[Peroxiredoxin 3D structures|Peroxiredoxin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11518528 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11518528}}
+__TOC__
+</StructureSection>
-==About this Structure==
-HD2 is a 1 chain 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=1HD2 OCA].
-==Reference==
-<ref group="xtra">PMID:11518528</ref><references group="xtra"/>
 [[Category: Homo sapiens]]
-[[Category: Declercq, J P.]]
+[[Category: Large Structures]]
-[[Category: Evrard, C.]]
+[[Category: Declercq JP]]
-[[Category: Antioxidant enzyme]]
+[[Category: Evrard C]]
-[[Category: Peroxiredoxin]]
-[[Category: Thioredoxin fold]]
-[[Category: Thioredoxin peroxidase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 14:22:00 2009''