3kp7: Difference between revisions

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OCA

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 ==Staphylococcus epidermidis TcaR (apo form)==
-<StructureSection load='3kp7' size='340' side='right' caption='[[3kp7]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='3kp7' size='340' side='right'caption='[[3kp7]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3kp7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Staeq Staeq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KP7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KP7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3kp7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_epidermidis_RP62A Staphylococcus epidermidis RP62A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KP7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KP7 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kp2|3kp2]], [[3kp3|3kp3]], [[3kp4|3kp4]], [[3kp5|3kp5]], [[3kp6|3kp6]]</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]] 2.3&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SERP1949, SE_1937, tcaR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176279 STAEQ])</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=3kp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kp7 OCA], [https://pdbe.org/3kp7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kp7 RCSB], [https://www.ebi.ac.uk/pdbsum/3kp7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kp7 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=3kp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kp7 OCA], [http://pdbe.org/3kp7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kp7 RCSB], [http://www.ebi.ac.uk/pdbsum/3kp7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kp7 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q5HLN6_STAEQ Q5HLN6_STAEQ]
 == 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/kp/3kp7_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kp/3kp7_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 18: / Line 19: @@
 </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=3kp7 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-TcaR and IcaR are a weak and a strong negative regulator of transcription of the ica locus, respectively, and their presence prevents the poly-N-acetylglucosamine production and biofilm formation in Staphylococcus epidermidis. Although TcaR was shown to interact with the ica promoter, the precise binding region and the mechanism of interaction remained unclear. Here we present the 3D structure of TcaR in its apo form and in complex with salicylate as well as several aminoglycoside and beta-lactam antibiotics. A comparison of the native and complex TcaR structures indicates that the mechanism of regulation involves a large conformational change in the DNA-binding lobe. Here, we deduced the consensus binding sequence of two [ approximately TTNNAA] hexamers embedded in a 16 bp sequence for a TcaR dimer. Six TcaR dimers bind specifically to three approximately 33 bp segments close to the IcaR binding region with varying affinities, and their repressor activity is directly interfered by salicylate and different classes of natural antimicrobial compounds. We also found in this study that the antimicrobial compounds we tested were shown not only to inhibit TcaR-DNA interaction but also to further induce biofilm formation in S. epidermidis in our in vivo assay. The results support a general mechanism for antibiotics in regulating TcaR-DNA interaction and thereby help understand the effect of antibiotic exposure on bacterial antibiotic resistance through biofilm formation.
-Structural study of TcaR and its complexes with multiple antibiotics from Staphylococcus epidermidis.,Chang YM, Jeng WY, Ko TP, Yeh YJ, Chen CK, Wang AH Proc Natl Acad Sci U S A. 2010 May 11;107(19):8617-22. Epub 2010 Apr 26. PMID:20421503<ref>PMID:20421503</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3kp7" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Staeq]]
+[[Category: Large Structures]]
-[[Category: Chang, Y M]]
+[[Category: Staphylococcus epidermidis RP62A]]
-[[Category: Chen, C K]]
+[[Category: Chang YM]]
-[[Category: Ko, T P]]
+[[Category: Chen CK]]
-[[Category: Wang, A H]]
+[[Category: Ko TP]]
-[[Category: Yeh, Y J]]
+[[Category: Wang AH]]
-[[Category: Biofilm]]
+[[Category: Yeh YJ]]
-[[Category: Dna binding]]
-[[Category: Multiple drug resistance]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Transcription regulator]]