1h0m: Difference between revisions

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-[[Image:1h0m.gif|left|200px]]<br />
-<applet load="1h0m" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1h0m, resolution 3.00&Aring;" />
-'''THREE-DIMENSIONAL STRUCTURE OF THE QUORUM SENSING PROTEIN TRAR BOUND TO ITS AUTOINDUCER AND TO ITS TARGET DNA'''<br />
-==Overview==
+==Three-dimensional structure of the quorum sensing protein TraR bound to its autoinducer and to its target DNA==
-The quorum sensing system allows bacteria to sense their cell density and, initiate an altered pattern of gene expression after a sufficient quorum, of cells has accumulated. In Agrobacterium tumefaciens, quorum sensing, controls conjugal transfer of the tumour- inducing plasmid, responsible, for plant crown gall disease. The core components of this system are the, transcriptional regulator TraR and its inducing ligand, N-(3-oxo-octanoyl)-L-homoserine lactone. This complex binds DNA and, activates gene expression. We have determined the crystal structure of, TraR in complex with its autoinducer and target DNA (PDB code 1h0m). The, protein is dimeric, with each monomer composed of an N-terminal domain, which binds the ligand in an enclosed cavity far from the dimerization, region, and a C-terminal domain, which binds DNA via a helix-turn-helix, motif. The structure reveals an asymmetric homodimer, with one monomer, longer than the other. The N-terminal domain resembles GAF/PAS domains, normally fused to catalytic signalling domains. In TraR, the gene fusion, is between a GAF/PAS domain and a DNA-binding domain, resulting in a, specific transcriptional regulator involved in quorum sensing.
+<StructureSection load='1h0m' size='340' side='right'caption='[[1h0m]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1h0m]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1H0M FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LAE:3-OXO-OCTANOIC+ACID+(2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE'>LAE</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1h0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h0m OCA], [https://pdbe.org/1h0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1h0m RCSB], [https://www.ebi.ac.uk/pdbsum/1h0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1h0m ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TRAR_RHIRD TRAR_RHIRD] Positive regulation of conjugal transfer of Ti plasmids. TraR activates target genes in the presence of AAI and also activates traR and traI themselves.
+== 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/h0/1h0m_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=1h0m ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-H0M is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens] with HSL as [http://en.wikipedia.org/wiki/ligand ligand]. Structure known Active Site: AA1. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1H0M OCA].
+*[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-The crystal structure of the quorum sensing protein TraR bound to its autoinducer and target DNA., Vannini A, Volpari C, Gargioli C, Muraglia E, Cortese R, De Francesco R, Neddermann P, Marco SD, EMBO J. 2002 Sep 2;21(17):4393-401. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12198141 12198141]
 [[Category: Agrobacterium tumefaciens]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Cortese, R.]]
+[[Category: Synthetic construct]]
-[[Category: Francesco, R.De.]]
+[[Category: Cortese R]]
-[[Category: Gargioli, C.]]
+[[Category: De Francesco R]]
-[[Category: Marco, S.Di.]]
+[[Category: Di Marco S]]
-[[Category: Muraglia, E.]]
+[[Category: Gargioli C]]
-[[Category: Neddermann, P.]]
+[[Category: Muraglia E]]
-[[Category: Vannini, A.]]
+[[Category: Neddermann P]]
-[[Category: Volpari, C.]]
+[[Category: Vannini A]]
-[[Category: HSL]]
+[[Category: Volpari C]]
-[[Category: dna-binding protein]]
-[[Category: homoserine lactone]]
-[[Category: luxr-type protein]]
-[[Category: quorum sensing]]
-[[Category: transcriptional regulator]]
-[[Category: trar]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov  5 16:24:52 2007''