3a9y: Difference between revisions

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-{{Seed}}
-[[Image:3a9y.jpg|left|200px]]
-<!--
+==Crystal structure of rat selenocysteine lyase in complex with L-cysteine==
-The line below this paragraph, containing "STRUCTURE_3a9y", creates the "Structure Box" on the page.
+<StructureSection load='3a9y' size='340' side='right'caption='[[3a9y]], [[Resolution|resolution]] 1.85&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'>[[3a9y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A9Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A9Y FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYS:CYSTEINE'>CYS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
--->
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3a9x|3a9x]], [[3a9z|3a9z]]</div></td></tr>
-{{STRUCTURE_3a9y|  PDB=3a9y  |  SCENE=  }}
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Scly ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Selenocysteine_lyase Selenocysteine lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.4.1.16 4.4.1.16] </span></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=3a9y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a9y OCA], [https://pdbe.org/3a9y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a9y RCSB], [https://www.ebi.ac.uk/pdbsum/3a9y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a9y ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[https://www.uniprot.org/uniprot/SCLY_RAT SCLY_RAT]] Catalyzes the decomposition of L-selenocysteine to L-alanine and elemental selenium (By similarity).
+== 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/a9/3a9y_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=3a9y ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Selenocysteine lyase (SCL) catalyzes the pyridoxal 5'-phosphate-dependent removal of selenium from l-selenocysteine to yield l-alanine. The enzyme is proposed to function in the recycling of the micronutrient selenium from degraded selenoproteins containing selenocysteine residue as an essential component. The enzyme exhibits strict substrate specificity toward l-selenocysteine and no activity to its cognate l-cysteine. However, it remains unclear how the enzyme distinguishes between selenocysteine and cysteine. Here, we present mechanistic studies of selenocysteine lyase from rat. ESI-MS analysis of wild-type and C375A mutant SCL revealed that the catalytic reaction proceeds via the formation of an enzyme-bound selenopersulfide intermediate on the catalytically essential Cys-375 residue. UV-visible spectrum analysis and the crystal structure of SCL complexed with l-cysteine demonstrated that the enzyme reversibly forms a nonproductive adduct with l-cysteine. Cys-375 on the flexible loop directed l-selenocysteine, but not l-cysteine, to the correct position and orientation in the active site to initiate the catalytic reaction. These findings provide, for the first time, the basis for understanding how trace amounts of a selenium-containing substrate is distinguished from excessive amounts of its cognate sulfur-containing compound in a biological system.
-===Crystal structure of rat selenocysteine lyase in complex with L-cysteine===
+Reaction mechanism and molecular basis for selenium/sulfur discrimination of selenocysteine lyase.,Omi R, Kurokawa S, Mihara H, Hayashi H, Goto M, Miyahara I, Kurihara T, Hirotsu K, Esaki N J Biol Chem. 2010 Apr 16;285(16):12133-9. Epub 2010 Feb 17. PMID:20164179<ref>PMID:20164179</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3a9y" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20164179}}, adds the Publication Abstract to the page
+*[[Selenocysteine lyase|Selenocysteine lyase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20164179 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20164179}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Buffalo rat]]
-A9Y is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A9Y OCA].
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:20164179</ref><references group="xtra"/>
-[[Category: Rattus norvegicus]]
 [[Category: Selenocysteine lyase]]
-[[Category: Hirotsu, K.]]
+[[Category: Hirotsu, K]]
-[[Category: Omi, R.]]
+[[Category: Omi, R]]
-[[Category: Cytoplasm]]
 [[Category: Lyase]]
 [[Category: Plp]]
@@ Line 34: / Line 48: @@
 [[Category: Selenocysteine]]
 [[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 17 09:29:31 2010''