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[[Image:1utb.gif|left|200px]]<br />
<applet load="1utb" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1utb, resolution 2.59&Aring;" />
'''DNTR FROM BURKHOLDERIA SP. STRAIN DNT'''<br />


==Overview==
==DntR from Burkholderia sp. strain DNT==
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.
<StructureSection load='1utb' size='340' side='right'caption='[[1utb]], [[Resolution|resolution]] 2.59&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1utb]] 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=1UTB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UTB 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]] 2.59&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=1utb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1utb OCA], [https://pdbe.org/1utb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1utb RCSB], [https://www.ebi.ac.uk/pdbsum/1utb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1utb ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q7WT50_9BURK Q7WT50_9BURK]
== 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/ut/1utb_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=1utb ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


==About this Structure==
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>
1UTB 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 ACT and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Structure known Active Site: AC1. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1UTB OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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]
</div>
[[Category: Burkholderia sp.]]
<div class="pdbe-citations 1utb" style="background-color:#fffaf0;"></div>
[[Category: Protein complex]]
== References ==
[[Category: Birse, D.]]
<references/>
[[Category: Brzezinski, P.]]
__TOC__
[[Category: Dian, C.]]
</StructureSection>
[[Category: Leonard, G.A.]]
[[Category: Burkholderia sp. DNT]]
[[Category: Mcsweeney, S.]]
[[Category: Large Structures]]
[[Category: Smirnova, I.A.]]
[[Category: Birse D]]
[[Category: ACT]]
[[Category: Brzezinski P]]
[[Category: GOL]]
[[Category: Dian C]]
[[Category: lysr]]
[[Category: Leonard GA]]
[[Category: transcriptional regulator]]
[[Category: McSweeney S]]
 
[[Category: Smirnova IA]]
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov  5 17:11:10 2007''

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