1jf9: Difference between revisions

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 ==Crystal Structure of selenocysteine lyase==
-<StructureSection load='1jf9' size='340' side='right' caption='[[1jf9]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='1jf9' size='340' side='right'caption='[[1jf9]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1jf9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JF9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JF9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1jf9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JF9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JF9 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
+</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&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NIFS/CSDB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Selenocysteine_lyase Selenocysteine lyase], with EC number [http://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=1jf9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jf9 OCA], [https://pdbe.org/1jf9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jf9 RCSB], [https://www.ebi.ac.uk/pdbsum/1jf9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jf9 ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/1jf9 TOPSAN]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jf9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jf9 OCA], [http://pdbe.org/1jf9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jf9 RCSB], [http://www.ebi.ac.uk/pdbsum/1jf9 PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/1jf9 TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SUFS_ECOLI SUFS_ECOLI]] Cysteine desulfurases mobilize the sulfur from L-cysteine to yield L-alanine, an essential step in sulfur metabolism for biosynthesis of a variety of sulfur-containing biomolecules. Component of the suf operon, which is activated and required under specific conditions such as oxidative stress and iron limitation. Acts as a potent selenocysteine lyase in vitro, that mobilizes selenium from L-selenocysteine. Selenocysteine lyase activity is however unsure in vivo.<ref>PMID:10829016</ref> <ref>PMID:12089140</ref> <ref>PMID:11997471</ref> <ref>PMID:12876288</ref> <ref>PMID:12941942</ref>
+[https://www.uniprot.org/uniprot/SUFS_ECOLI SUFS_ECOLI] Cysteine desulfurases mobilize the sulfur from L-cysteine to yield L-alanine, an essential step in sulfur metabolism for biosynthesis of a variety of sulfur-containing biomolecules. Component of the suf operon, which is activated and required under specific conditions such as oxidative stress and iron limitation. Acts as a potent selenocysteine lyase in vitro, that mobilizes selenium from L-selenocysteine. Selenocysteine lyase activity is however unsure in vivo.<ref>PMID:10829016</ref> <ref>PMID:12089140</ref> <ref>PMID:11997471</ref> <ref>PMID:12876288</ref> <ref>PMID:12941942</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/jf/1jf9_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jf/1jf9_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 20: / Line 20: @@
 </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=1jf9 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The Escherichia coli NifS CsdB protein is a member of the homodimeric pyridoxal 5'-phosphate (PLP)-dependent family of enzymes. These enzymes are capable of decomposing cysteine or selenocysteine into L-alanine and sulfur or selenium, respectively. E. coli NifS CsdB has a high specificity for L-selenocysteine in comparison to l-cysteine, suggesting a role for this enzyme is selenium metabolism. The 2.0 A crystal structure of E. coli NifS CsdB reveals a high-resolution view of the active site of this enzyme in apo-, persulfide, perselenide, and selenocysteine-bound intermediates, suggesting a mechanism for the stabilization of the enzyme persulfide and perselenide intermediates during catalysis, a necessary intermediate in the formation of sulfur and selenium containing metabolites.
-Analysis of the E. coli NifS CsdB protein at 2.0 A reveals the structural basis for perselenide and persulfide intermediate formation.,Lima CD J Mol Biol. 2002 Feb 1;315(5):1199-208. PMID:11827487<ref>PMID:11827487</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+==See Also==
-</div>
+*[[Selenocysteine lyase|Selenocysteine lyase]]
-<div class="pdbe-citations 1jf9" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Selenocysteine lyase]]
+[[Category: Large Structures]]
-[[Category: Burley, S K]]
+[[Category: Burley SK]]
-[[Category: Lima, C D]]
+[[Category: Lima CD]]
-[[Category: Structural genomic]]
-[[Category: Cysteine]]
-[[Category: Lyase]]
-[[Category: Nif]]
-[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Pursulfide]]
-[[Category: Selenocysteine]]