3ehg: Difference between revisions

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 ==Crystal structure of the ATP-binding domain of DesK in complex with ATP==
-<StructureSection load='3ehg' size='340' side='right' caption='[[3ehg]], [[Resolution|resolution]] 1.74&Aring;' scene=''>
+<StructureSection load='3ehg' size='340' side='right'caption='[[3ehg]], [[Resolution|resolution]] 1.74&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ehg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EHG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EHG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ehg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EHG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EHG FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.74&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ehf|3ehf]], [[3ehh|3ehh]], [[3ehj|3ehj]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yocF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=3ehg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ehg OCA], [https://pdbe.org/3ehg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ehg RCSB], [https://www.ebi.ac.uk/pdbsum/3ehg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ehg ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </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=3ehg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ehg OCA], [http://pdbe.org/3ehg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ehg RCSB], [http://www.ebi.ac.uk/pdbsum/3ehg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ehg ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DESK_BACSU DESK_BACSU]] Member of the two-component regulatory system DesR/DesK, responsible for cold induction of the des gene coding for the Delta5 acyl-lipid desaturase. Acts as a sensor of the membrane fluidity. Probably activates DesR by phosphorylation.<ref>PMID:11285232</ref> <ref>PMID:11717295</ref> <ref>PMID:12207704</ref> <ref>PMID:14734164</ref> <ref>PMID:15090506</ref>
+[https://www.uniprot.org/uniprot/DESK_BACSU DESK_BACSU] Member of the two-component regulatory system DesR/DesK, responsible for cold induction of the des gene coding for the Delta5 acyl-lipid desaturase. Acts as a sensor of the membrane fluidity. Probably activates DesR by phosphorylation.<ref>PMID:11285232</ref> <ref>PMID:11717295</ref> <ref>PMID:12207704</ref> <ref>PMID:14734164</ref> <ref>PMID:15090506</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 22: / 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=3ehg ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-DesK is a sensor histidine kinase (HK) that allows Bacillus subtilis to respond to cold shock, triggering the adaptation of membrane fluidity via transcriptional control of a fatty acid desaturase. It belongs to the HK family HPK7, which includes the nitrogen metabolism regulators NarX/Q and the antibiotic sensor LiaS among other important sensor kinases. Structural information on different HK families is still scarce and several questions remain, particularly concerning the molecular features that determine HK specificity during its catalytic autophosphorylation and subsequent response-regulator phosphotransfer reactions. To analyze the ATP-binding features of HPK7 HKs and dissect their mechanism of autophosphorylation at the molecular level, we have studied DesK in complex with ATP using high resolution structural approaches in combination with biochemical studies. We report the first crystal structure of an HK in complex with its natural nucleotidic substrate. The general fold of the ATP-binding domain of DesK is conserved, compared with well studied members of other families. Yet, DesK displays a far more compact structure at the ATP-binding pocket: the ATP lid loop is much shorter with no secondary structural organization and becomes ordered upon ATP loading. Sequence conservation mapping onto the molecular surface, semi-flexible protein-protein docking simulations, and structure-based point mutagenesis allow us to propose a specific domain-domain geometry during autophosphorylation catalysis. Supporting our hypotheses, we have been able to trap an autophosphorylating intermediate state, by protein engineering at the predicted domain-domain interaction surface.
-Structural and enzymatic insights into the ATP binding and autophosphorylation mechanism of a sensor histidine kinase.,Trajtenberg F, Grana M, Ruetalo N, Botti H, Buschiazzo A J Biol Chem. 2010 Aug 6;285(32):24892-903. Epub 2010 May 27. PMID:20507988<ref>PMID:20507988</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3ehg" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Vibrio subtilis ehrenberg 1835]]
+[[Category: Bacillus subtilis]]
-[[Category: Histidine kinase]]
+[[Category: Large Structures]]
-[[Category: Buschiazzo, A]]
+[[Category: Buschiazzo A]]
-[[Category: Trajtenberg, F]]
+[[Category: Trajtenberg F]]
-[[Category: Ghl atpase domain]]
-[[Category: Kinase]]
-[[Category: Transferase]]