2hq5: Difference between revisions

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-{{Seed}}
-[[Image:2hq5.png|left|200px]]
-<!--
+==Crystal structure of multidrug binding protein QacR from Staphylococcus aureus cocrystallized with compound DB359==
-The line below this paragraph, containing "STRUCTURE_2hq5", creates the "Structure Box" on the page.
+<StructureSection load='2hq5' size='340' side='right'caption='[[2hq5]], [[Resolution|resolution]] 2.80&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'>[[2hq5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HQ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HQ5 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</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>
-{{STRUCTURE_2hq5|  PDB=2hq5  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2hq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hq5 OCA], [https://pdbe.org/2hq5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hq5 RCSB], [https://www.ebi.ac.uk/pdbsum/2hq5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hq5 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/QACR_STAAU QACR_STAAU] Transcriptional repressor of qacA. Binds to IR1, an unusually long 28 bp operator, which is located downstream from the qacA promoter and overlaps its transcription start site. QacR is induced from its IR1 site by binding to one of many structurally dissimilar cationic lipophilic compounds, which are also substrates of QacA.
+== 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/hq/2hq5_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=2hq5 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Staphylococcus aureus QacR is a multidrug-binding transcription repressor. Crystal structures of multiple QacR-drug complexes reveal that these toxins bind in a large pocket, which is composed of smaller overlapping "minipockets". Stacking, van der Waals, and ionic interactions are common features of binding, whereas hydrogen bonds are limited. Pentamidine, a bivalent aromatic diamidine, interacts with QacR differently as one positively charged benzamidine moiety is neutralized by the dipoles of side-chain and peptide backbone oxygens rather than a formal negative charge from proximal acidic residues. To understand the binding mechanisms of other bivalent benzamidines, we determined the crystal structures of the QacR-DB75 and QacR-DB359 complexes and measured their binding affinities. Although these rigid aromatic diamidines bind with low-micromolar affinities, they do not use single, discrete binding modes. Such promiscuous binding underscores the intrinsic chemical redundancy of the QacR multidrug-binding pocket. Chemical redundancy is likely a hallmark of all multidrug-binding pockets, yet it is utilized by only a subset of drugs, which, for QacR, so far appears to be limited to chemically rigid, bivalent compounds.
-===Crystal structure of multidrug binding protein QacR from Staphylococcus aureus cocrystallized with compound DB359===
+Multidrug-binding transcription factor QacR binds the bivalent aromatic diamidines DB75 and DB359 in multiple positions.,Brooks BE, Piro KM, Brennan RG J Am Chem Soc. 2007 Jul 4;129(26):8389-95. Epub 2007 Jun 13. PMID:17567017<ref>PMID:17567017</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2hq5" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17567017}}, adds the Publication Abstract to the page
+*[[Tetracycline repressor protein 3D structures|Tetracycline repressor protein 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17567017 is the PubMed ID number.
+*[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_17567017}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-HQ5 is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HQ5 OCA].
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:17567017</ref><references group="xtra"/>
 [[Category: Staphylococcus aureus]]
-[[Category: Brennan, R G.]]
+[[Category: Brennan RG]]
-[[Category: Brooks, B E.]]
+[[Category: Brooks BE]]
-[[Category: Db359]]
-[[Category: Multidrug binding protein]]
-[[Category: Multidrug recognition]]
-[[Category: Qacr]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 14:57:11 2009''