1l3l

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(New page: 200px<br /><applet load="1l3l" size="450" color="white" frame="true" align="right" spinBox="true" caption="1l3l, resolution 1.66&Aring;" /> '''Crystal structure of...)
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[[Image:1l3l.gif|left|200px]]<br /><applet load="1l3l" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1l3l, resolution 1.66&Aring;" />
 
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'''Crystal structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA'''<br />
 
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==Overview==
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==Crystal structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA==
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Many proteobacteria are able to monitor their population densities through, the release of pheromones known as N-acylhomoserine lactones. At high, population densities, these pheromones elicit diverse responses that, include bioluminescence, biofilm formation, production of antimicrobials, DNA exchange, pathogenesis and symbiosis. Many of these regulatory systems, require a pheromone-dependent transcription factor similar to the LuxR, protein of Vibrio fischeri. Here we present the structure of a LuxR-type, protein. TraR of Agrobacterium tumefaciens was solved at 1.66 A as a, complex with the pheromone N-3-oxooctanoyl-L-homoserine lactone (OOHL) and, its TraR DNA-binding site. The amino-terminal domain of TraR is an, alpha/beta/alpha sandwich that binds OOHL, whereas the carboxy-terminal, domain contains a helix turn helix DNA-binding motif. The TraR dimer, displays a two-fold symmetry axis in each domain; however, these two axes, of symmetry are at an approximately 90 degree angle, resulting in a, pronounced overall asymmetry of the complex. The pheromone lies fully, embedded within the protein with virtually no solvent contact, and makes, numerous hydrophobic contacts with the protein as well as four hydrogen, bonds: three direct and one water-mediated.
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<StructureSection load='1l3l' size='340' side='right'caption='[[1l3l]], [[Resolution|resolution]] 1.66&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1l3l]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L3L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L3L FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.66&#8491;</td></tr>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1l3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l3l OCA], [https://pdbe.org/1l3l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l3l RCSB], [https://www.ebi.ac.uk/pdbsum/1l3l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l3l ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l3/1l3l_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1l3l ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Many proteobacteria are able to monitor their population densities through the release of pheromones known as N-acylhomoserine lactones. At high population densities, these pheromones elicit diverse responses that include bioluminescence, biofilm formation, production of antimicrobials, DNA exchange, pathogenesis and symbiosis. Many of these regulatory systems require a pheromone-dependent transcription factor similar to the LuxR protein of Vibrio fischeri. Here we present the structure of a LuxR-type protein. TraR of Agrobacterium tumefaciens was solved at 1.66 A as a complex with the pheromone N-3-oxooctanoyl-L-homoserine lactone (OOHL) and its TraR DNA-binding site. The amino-terminal domain of TraR is an alpha/beta/alpha sandwich that binds OOHL, whereas the carboxy-terminal domain contains a helix turn helix DNA-binding motif. The TraR dimer displays a two-fold symmetry axis in each domain; however, these two axes of symmetry are at an approximately 90 degree angle, resulting in a pronounced overall asymmetry of the complex. The pheromone lies fully embedded within the protein with virtually no solvent contact, and makes numerous hydrophobic contacts with the protein as well as four hydrogen bonds: three direct and one water-mediated.
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==About this Structure==
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Structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA.,Zhang RG, Pappas T, Brace JL, Miller PC, Oulmassov T, Molyneaux JM, Anderson JC, Bashkin JK, Winans SC, Joachimiak A Nature. 2002 Jun 27;417(6892):971-4. PMID:12087407<ref>PMID:12087407</ref>
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1L3L is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens] with LAE as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1L3L OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA., Zhang RG, Pappas T, Brace JL, Miller PC, Oulmassov T, Molyneaux JM, Anderson JC, Bashkin JK, Winans SC, Joachimiak A, Nature. 2002 Jun 27;417(6892):971-4. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12087407 12087407]
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</div>
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[[Category: Agrobacterium tumefaciens]]
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<div class="pdbe-citations 1l3l" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Anderson, J.C.]]
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[[Category: Bashkin, J.K.]]
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[[Category: Brace, J.L.]]
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[[Category: Joachimiak, A.]]
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[[Category: Miller, P.C.]]
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[[Category: Molyneaux, J.M.]]
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[[Category: Oulmassov, T.]]
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[[Category: Pappas, T.]]
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[[Category: Winans, S.C.]]
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[[Category: Zhang, R.]]
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[[Category: LAE]]
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[[Category: alpha/beta/alpha sandwich]]
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[[Category: asymmetry of the protein-dna complex]]
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[[Category: helix-turn-helix dna binding motif]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 20:13:20 2007''
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==See Also==
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*[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Agrobacterium tumefaciens]]
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[[Category: Large Structures]]
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[[Category: Anderson JC]]
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[[Category: Bashkin JK]]
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[[Category: Brace JL]]
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[[Category: Joachimiak A]]
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[[Category: Miller PC]]
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[[Category: Molyneaux JM]]
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[[Category: Oulmassov T]]
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[[Category: Pappas T]]
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[[Category: Winans SC]]
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[[Category: Zhang R]]

Current revision

Crystal structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA

PDB ID 1l3l

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