1uth

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[[Image:1uth.jpg|left|200px]]<br /><applet load="1uth" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1uth, resolution 2.20&Aring;" />
 
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'''DNTR FROM BURKHOLDERIA SP. STRAIN DNT IN COMPLEX WITH THIOCYANATE'''<br />
 
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==Overview==
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==DntR from Burkholderia sp. strain DNT in complex with Thiocyanate==
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The transcriptional regulator DntR, a member of the LysR family, is a, central element in a prototype bacterial cell-based biosensor for the, detection of hazardous contamination of soil and groundwater by, dinitrotoluenes. To optimise the sensitivity of the biosensor for such, compounds we have chosen a rational design of the inducer-binding cavity, based on knowledge of the three-dimensional structure of DntR. We report, two crystal structures of DntR with acetate (resolution 2.6 angstroms) and, thiocyanate (resolution 2.3 angstroms), respectively, occupying the, inducer-binding cavity. These structures allow for the construction of, models of DntR in complex with salicylate (Kd approximately or = 4 microM), and 2,4-dinitrotoluene that provide a basis for the design of mutant DntR, with enhanced specificity for dinitrotoluenes. In both crystal structures, DntR crystallises as a homodimer with a "head-to-tail" arrangement of, monomers in the asymmetric unit. Analysis of the crystal structure has, allowed the building of a full-length model of DntR in its biologically, active homotetrameric form consisting of two "head-to-head" dimers. The, implications of this model for the mechanism of transcription regulation, by LysR proteins are discussed.
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<StructureSection load='1uth' size='340' side='right'caption='[[1uth]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1uth]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_sp._DNT Burkholderia sp. DNT]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UTH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UTH 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]] 2.2&#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=SCN:THIOCYANATE+ION'>SCN</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=1uth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uth OCA], [https://pdbe.org/1uth PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uth RCSB], [https://www.ebi.ac.uk/pdbsum/1uth PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uth ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q7WT50_9BURK Q7WT50_9BURK]
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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/ut/1uth_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1uth 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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The transcriptional regulator DntR, a member of the LysR family, is a central element in a prototype bacterial cell-based biosensor for the detection of hazardous contamination of soil and groundwater by dinitrotoluenes. To optimise the sensitivity of the biosensor for such compounds we have chosen a rational design of the inducer-binding cavity based on knowledge of the three-dimensional structure of DntR. We report two crystal structures of DntR with acetate (resolution 2.6 angstroms) and thiocyanate (resolution 2.3 angstroms), respectively, occupying the inducer-binding cavity. These structures allow for the construction of models of DntR in complex with salicylate (Kd approximately or = 4 microM) and 2,4-dinitrotoluene that provide a basis for the design of mutant DntR with enhanced specificity for dinitrotoluenes. In both crystal structures DntR crystallises as a homodimer with a "head-to-tail" arrangement of monomers in the asymmetric unit. Analysis of the crystal structure has allowed the building of a full-length model of DntR in its biologically active homotetrameric form consisting of two "head-to-head" dimers. The implications of this model for the mechanism of transcription regulation by LysR proteins are discussed.
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==About this Structure==
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Development of a bacterial biosensor for nitrotoluenes: the crystal structure of the transcriptional regulator DntR.,Smirnova IA, Dian C, Leonard GA, McSweeney S, Birse D, Brzezinski P J Mol Biol. 2004 Jul 9;340(3):405-18. PMID:15210343<ref>PMID:15210343</ref>
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1UTH is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Burkholderia_sp. Burkholderia sp.] with <scene name='pdbligand=SCN:'>SCN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Known structural/functional Site: <scene name='pdbsite=AC1:Scn+Binding+Site+For+Chain+A'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UTH 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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Development of a bacterial biosensor for nitrotoluenes: the crystal structure of the transcriptional regulator DntR., Smirnova IA, Dian C, Leonard GA, McSweeney S, Birse D, Brzezinski P, J Mol Biol. 2004 Jul 9;340(3):405-18. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15210343 15210343]
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</div>
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[[Category: Burkholderia sp.]]
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<div class="pdbe-citations 1uth" style="background-color:#fffaf0;"></div>
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[[Category: Protein complex]]
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[[Category: Birse, D.]]
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[[Category: Brzezinski, P.]]
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[[Category: Dian, C.]]
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[[Category: Leonard, G.A.]]
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[[Category: Mcsweeney, S.]]
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[[Category: Smirnova, I.A.]]
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[[Category: SCN]]
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[[Category: lysr]]
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[[Category: transcriptional regulator]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 10:04:44 2008''
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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: Burkholderia sp. DNT]]
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[[Category: Large Structures]]
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[[Category: Birse D]]
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[[Category: Brzezinski P]]
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[[Category: Dian C]]
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[[Category: Leonard GA]]
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[[Category: McSweeney S]]
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[[Category: Smirnova IA]]

Current revision

DntR from Burkholderia sp. strain DNT in complex with Thiocyanate

PDB ID 1uth

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