1utb: Difference between revisions

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-{{Seed}}
-[[Image:1utb.png|left|200px]]
-<!--
+==DntR from Burkholderia sp. strain DNT==
-The line below this paragraph, containing "STRUCTURE_1utb", creates the "Structure Box" on the page.
+<StructureSection load='1utb' size='340' side='right'caption='[[1utb]], [[Resolution|resolution]] 2.59&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</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>
-{{STRUCTURE_1utb|  PDB=1utb  |  SCENE=  }}
+<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.
-===DNTR FROM BURKHOLDERIA SP. STRAIN DNT===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_15210343}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1utb" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 15210343 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15210343}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Burkholderia sp. DNT]]
-UTB is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Burkholderia_sp. Burkholderia sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UTB OCA].
+[[Category: Large Structures]]
+[[Category: Birse D]]
-==Reference==
+[[Category: Brzezinski P]]
-<ref group="xtra">PMID:15210343</ref><references group="xtra"/>
+[[Category: Dian C]]
-[[Category: Burkholderia sp.]]
+[[Category: Leonard GA]]
-[[Category: Birse, D.]]
+[[Category: McSweeney S]]
-[[Category: Brzezinski, P.]]
+[[Category: Smirnova IA]]
-[[Category: Dian, C.]]
-[[Category: Leonard, G A.]]
-[[Category: Mcsweeney, S.]]
-[[Category: Smirnova, I A.]]
-[[Category: Lysr]]
-[[Category: Transcriptional regulator]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 12:48:01 2009''