3hrs: Difference between revisions

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OCA

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 ==Crystal Structure of the Manganese-activated Repressor ScaR: apo form==
-<StructureSection load='3hrs' size='340' side='right' caption='[[3hrs]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+<StructureSection load='3hrs' size='340' side='right'caption='[[3hrs]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3hrs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_10558 Atcc 10558]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HRS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HRS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3hrs]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_gordonii Streptococcus gordonii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HRS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HRS FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.7&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3hrt|3hrt]], [[3hru|3hru]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">scaR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1302 ATCC 10558])</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=3hrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hrs OCA], [https://pdbe.org/3hrs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hrs RCSB], [https://www.ebi.ac.uk/pdbsum/3hrs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hrs ProSAT]</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=3hrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hrs OCA], [http://pdbe.org/3hrs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hrs RCSB], [http://www.ebi.ac.uk/pdbsum/3hrs PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9RFN3_STRGN Q9RFN3_STRGN]
 == 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/hr/3hrs_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hr/3hrs_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 18: / 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=3hrs ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The streptococcal coaggregation regulator (ScaR) of Streptococcus gordonii is a manganese-dependent transcriptional regulator. When intracellular manganese concentrations become elevated, ScaR represses transcription of the scaCBA operon, which encodes a manganese uptake transporter. A member of the DtxR/MntR family of metalloregulators, ScaR shares sequence similarity with other family members, and many metal-binding residues are conserved. Here, we show that ScaR is an active dimer, with two dimers binding the 46 base pair scaC operator. Each ScaR subunit binds two manganese ions, and the protein is activated by a variety of other metal ions, including Cd(2+), Co(2+), and Ni(2+) but not Zn(2+). The crystal structure of apo-ScaR reveals a tertiary and quaternary structure similar to its homologue, the iron-responsive regulator DtxR. While each DtxR subunit binds a metal ion in two sites, labeled primary and ancillary, crystal structures of ScaR determined in the presence of Cd(2+) and Zn(2+) show only a single occupied metal-binding site that is novel to ScaR. The site analogous to the primary site in DtxR is unoccupied, and the ancillary site is absent from ScaR. Instead, metal ions bind to ScaR at a site labeled "secondary", which is composed of Glu80, Cys123, His125, and Asp160 and lies roughly 5 A away from where the ancillary site would be predicted to exist. This difference suggests that ScaR and its closely related homologues are activated by a mechanism distinct from that of either DtxR or MntR.
-Characterization and structure of the manganese-responsive transcriptional regulator ScaR.,Stoll KE, Draper WE, Kliegman JI, Golynskiy MV, Brew-Appiah RA, Phillips RK, Brown HK, Breyer WA, Jakubovics NS, Jenkinson HF, Brennan RG, Cohen SM, Glasfeld A Biochemistry. 2009 Nov 3;48(43):10308-20. PMID:19795834<ref>PMID:19795834</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3hrs" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 10558]]
+[[Category: Large Structures]]
-[[Category: Brennan, R B]]
+[[Category: Streptococcus gordonii]]
-[[Category: Brew-Appiah, R A.T]]
+[[Category: Brennan RB]]
-[[Category: Breyer, W A]]
+[[Category: Brew-Appiah RAT]]
-[[Category: Brown, H K]]
+[[Category: Breyer WA]]
-[[Category: Cohen, S M]]
+[[Category: Brown HK]]
-[[Category: Draper, W E]]
+[[Category: Cohen SM]]
-[[Category: Glasfeld, A]]
+[[Category: Draper WE]]
-[[Category: Golynskiy, M V]]
+[[Category: Glasfeld A]]
-[[Category: Jakubovics, N S]]
+[[Category: Golynskiy MV]]
-[[Category: Jenkinson, H F]]
+[[Category: Jakubovics NS]]
-[[Category: Kliegman, J I]]
+[[Category: Jenkinson HF]]
-[[Category: Stoll, K E]]
+[[Category: Kliegman JI]]
-[[Category: Dtxr/mntr family member]]
+[[Category: Stoll KE]]
-[[Category: Transcription]]