4if4: Difference between revisions

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 ==Crystal Structure of the Magnesium and beryllofluoride-activated VraR from Staphylococcus aureus==
-<StructureSection load='4if4' size='340' side='right' caption='[[4if4]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
+<StructureSection load='4if4' size='340' side='right'caption='[[4if4]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4if4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Staam Staam]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IF4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IF4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4if4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_Mu50 Staphylococcus aureus subsp. aureus Mu50]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IF4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IF4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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]] 2.35&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4gvp|4gvp]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SAV1884, vraR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=158878 STAAM])</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=4if4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4if4 OCA], [https://pdbe.org/4if4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4if4 RCSB], [https://www.ebi.ac.uk/pdbsum/4if4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4if4 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=4if4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4if4 OCA], [http://pdbe.org/4if4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4if4 RCSB], [http://www.ebi.ac.uk/pdbsum/4if4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4if4 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/VRAR_STAAM VRAR_STAAM]] Member of the two-component regulatory system VraS/VraR involved in the control of the cell wall peptidoglycan biosynthesis. VraR is overexpressed in strain Mu50, which leads to vancomycin resistance.
+[https://www.uniprot.org/uniprot/VRAR_STAAM VRAR_STAAM] Member of the two-component regulatory system VraS/VraR involved in the control of the cell wall peptidoglycan biosynthesis. VraR is overexpressed in strain Mu50, which leads to vancomycin resistance.
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Staphylococcus aureus VraR, a vancomycin-resistance-associated response regulator, activates a cell-wall-stress stimulon in response to antibiotics that inhibit cell wall formation. X-ray crystal structures of VraR in both unphosphorylated and beryllofluoride-activated states have been determined, revealing a mechanism of phosphorylation-induced dimerization that features a deep hydrophobic pocket at the center of the receiver domain interface. Unphosphorylated VraR exists in a closed conformation that inhibits dimer formation. Phosphorylation at the active site promotes conformational changes that are propagated throughout the receiver domain, promoting the opening of a hydrophobic pocket that is essential for homodimer formation and enhanced DNA-binding activity. This prominent feature in the VraR dimer can potentially be exploited for the development of novel therapeutics to counteract antibiotic resistance in this important pathogen.
-Phosphorylation-dependent conformational changes and domain rearrangements in Staphylococcus aureus VraR activation.,Leonard PG, Golemi-Kotra D, Stock AM Proc Natl Acad Sci U S A. 2013 May 21;110(21):8525-30. doi:, 10.1073/pnas.1302819110. Epub 2013 May 6. PMID:23650349<ref>PMID:23650349</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4if4" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Response regulator|Response regulator]]
+*[[Response regulator 3D structure|Response regulator 3D structure]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Staam]]
+[[Category: Large Structures]]
-[[Category: Leonard, P G]]
+[[Category: Staphylococcus aureus subsp. aureus Mu50]]
-[[Category: Stock, A M]]
+[[Category: Leonard PG]]
-[[Category: Bacterial signalling]]
+[[Category: Stock AM]]
-[[Category: Dna binding]]
-[[Category: Phosphorylation]]
-[[Category: Response regulator]]
-[[Category: Transcription]]
-[[Category: Transcription factor]]
-[[Category: Transcription regulation]]
-[[Category: Two-component system]]