3by9: Difference between revisions

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-{{Seed}}
-[[Image:3by9.png|left|200px]]
-<!--
+==Crystal structure of the V. cholerae Histidine Kinase DctB Sensor Domain==
-The line below this paragraph, containing "STRUCTURE_3by9", creates the "Structure Box" on the page.
+<StructureSection load='3by9' size='340' side='right'caption='[[3by9]], [[Resolution|resolution]] 1.70&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'>[[3by9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BY9 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]] 1.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></td></tr>
-{{STRUCTURE_3by9|  PDB=3by9  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3by9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3by9 OCA], [https://pdbe.org/3by9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3by9 RCSB], [https://www.ebi.ac.uk/pdbsum/3by9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3by9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9KQS3_VIBCH Q9KQS3_VIBCH]
+== 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/by/3by9_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3by9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Two-component signaling systems allow bacteria to adapt to changing environments. Typically, a chemical or other stimulus is detected by the periplasmic sensor domain of a transmembrane histidine kinase sensor, which in turn relays a signal through a phosphotransfer cascade to the cognate cytoplasmic response regulator. Such systems lead ultimately to changes in gene expression or cell motility. Mechanisms of ligand binding and signal transduction through the cell membrane in histidine kinases are not fully understood. In an effort to further understand such processes, we have solved the crystal structures of the periplasmic sensor domains of Escherichia coli DcuS and of Vibrio cholerae DctB in complex with the respective cognate ligands, malate and succinate. Both proteins are involved in the regulation of the transport and metabolism of C(4)-dicarboxylates, but they are not highly related by sequence similarity. Our work reveals that despite disparate sizes, both structures contain a similar characteristic alpha/beta PDC (PhoQ-DcuS-CitA) sensor-domain fold and display similar modes of ligand binding, suggesting similar mechanisms of function.
-===Crystal Structure of the E. coli Histidine Kinase DcuS Sensor Domain===
+Crystal structures of C4-dicarboxylate ligand complexes with sensor domains of histidine kinases DcuS and DctB.,Cheung J, Hendrickson WA J Biol Chem. 2008 Oct 31;283(44):30256-65. Epub 2008 Aug 12. PMID:18701447<ref>PMID:18701447</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-==About this Structure==
+</div>
-BY9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BY9 OCA].
+<div class="pdbe-citations 3by9" style="background-color:#fffaf0;"></div>
-[[Category: Histidine kinase]]
+== References ==
-[[Category: Single protein]]
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Vibrio cholerae]]
-[[Category: Cheung, J.]]
+[[Category: Cheung J]]
-[[Category: Hendrickson, W A.]]
+[[Category: Hendrickson WA]]
-[[Category: Histidine kinase sensor domain]]
-[[Category: Phosphoprotein]]
-[[Category: Transferase]]
-[[Category: Two-component regulatory system]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 27 10:39:57 2008''