1dp2: Difference between revisions

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-[[Image:1dp2.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1dp2", creates the "Structure Box" on the page.
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-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_1dp2|  PDB=1dp2  |  SCENE=  }}
-'''CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN RHODANESE AND LIPOATE'''
+==CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN RHODANESE AND LIPOATE==
+<StructureSection load='1dp2' size='340' side='right'caption='[[1dp2]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1dp2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DP2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DP2 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.01&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene>, <scene name='pdbligand=LPB:5-[(3S)-1,2-DITHIOLAN-3-YL]PENTANOIC+ACID'>LPB</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=1dp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dp2 OCA], [https://pdbe.org/1dp2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dp2 RCSB], [https://www.ebi.ac.uk/pdbsum/1dp2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dp2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/THTR_BOVIN THTR_BOVIN] Together with MRPL18, acts as a mitochondrial import factor for the cytosolic 5S rRNA. Only the nascent unfolded cytoplasmic form is able to bind to the 5S rRNA (By similarity). Formation of iron-sulfur complexes and cyanide detoxification. Binds molecular oxygen and sulfur.
+== 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/dp/1dp2_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=1dp2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Dihydrolipoate is an acceptor of the rhodanese-bound sulfane sulfur atom, as shown by analysis of the elementary steps of the reaction catalyzed by rhodanese. The crystal structure of sulfur-substituted rhodanese complexed with the non-reactive oxidized form of lipoate has revealed that the compound is bound at the enzyme active site, with the dithiolane ring buried in the interior of the cavity and the carboxylic end pointing towards the solvent. One of the sulfur atoms of the ligand in the unproductive complex is relatively close to the sulfane sulfur bound to Cys-247, the sulfur that is transferred during the catalytic reaction. This mode of binding of lipoate is likely to mimic that of dihydrolipoate. The results presented here support the possible role of dihydrolipoate as sulfur-acceptor substrate of rhodanese in an enzymatic reaction that might serve to provide iron-sulfur proteins with inorganic sulfide.
-==Overview==
+Specific interaction of lipoate at the active site of rhodanese.,Cianci M, Gliubich F, Zanotti G, Berni R Biochim Biophys Acta. 2000 Aug 31;1481(1):103-8. PMID:11004580<ref>PMID:11004580</ref>
-Dihydrolipoate is an acceptor of the rhodanese-bound sulfane sulfur atom, as shown by analysis of the elementary steps of the reaction catalyzed by rhodanese. The crystal structure of sulfur-substituted rhodanese complexed with the non-reactive oxidized form of lipoate has revealed that the compound is bound at the enzyme active site, with the dithiolane ring buried in the interior of the cavity and the carboxylic end pointing towards the solvent. One of the sulfur atoms of the ligand in the unproductive complex is relatively close to the sulfane sulfur bound to Cys-247, the sulfur that is transferred during the catalytic reaction. This mode of binding of lipoate is likely to mimic that of dihydrolipoate. The results presented here support the possible role of dihydrolipoate as sulfur-acceptor substrate of rhodanese in an enzymatic reaction that might serve to provide iron-sulfur proteins with inorganic sulfide.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-DP2 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DP2 OCA].
+</div>
+<div class="pdbe-citations 1dp2" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Specific interaction of lipoate at the active site of rhodanese., Cianci M, Gliubich F, Zanotti G, Berni R, Biochim Biophys Acta. 2000 Aug 31;1481(1):103-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11004580 11004580]
+*[[Sulfurtransferase|Sulfurtransferase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Bos taurus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Thiosulfate sulfurtransferase]]
+[[Category: Cianci M]]
-[[Category: Cianci, M.]]
+[[Category: Zanotti G]]
-[[Category: Zanotti, G.]]
-[[Category: Liopate]]
-[[Category: Rhodanese]]
-[[Category: Sulfurtransferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 14:06:09 2008''