2k1n: Difference between revisions

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-{{Seed}}
-[[Image:2k1n.png|left|200px]]
-<!--
+==DNA bound structure of the N-terminal domain of AbrB==
-The line below this paragraph, containing "STRUCTURE_2k1n", creates the "Structure Box" on the page.
+<StructureSection load='2k1n' size='340' side='right'caption='[[2k1n]]' 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'>[[2k1n]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K1N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K1N 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">Solution NMR, 10 models</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=2k1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k1n OCA], [https://pdbe.org/2k1n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k1n RCSB], [https://www.ebi.ac.uk/pdbsum/2k1n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k1n ProSAT]</span></td></tr>
-{{STRUCTURE_2k1n|  PDB=2k1n  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ABRB_BACSU ABRB_BACSU] Ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation. It controls the expression of genes spovG and tycA. AbrB binds to the tycA promoter region at two A- and T-rich sites, it may be the sole repressor of tycA transcription.<ref>PMID:2504584</ref>
+== 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/k1/2k1n_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2k1n ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Understanding the DNA recognition and binding by the AbrB-like family of transcriptional regulators is of significant interest since these proteins enable bacteria to elicit the appropriate response to diverse environmental stimuli. Although these "transition-state regulator" proteins have been well characterized at the genetic level, the general and specific mechanisms of DNA binding remain elusive. We present RDC-refined NMR solution structures and dynamic properties of the DNA-binding domains of three Bacillus subtilis transition-state regulators: AbrB, Abh, and SpoVT. We combined previously investigated DNase I footprinting, DNA methylation, gel-shift assays, and mutagenic and NMR studies to generate a structural model of the complex between AbrBN(55) and its cognate promoter, abrB8. These investigations have enabled us to generate a model for the specific nature of the transition-state regulator-DNA interaction, a structure that has remained elusive thus far.
-===DNA bound structure of the N-terminal domain of AbrB===
+Insights into the nature of DNA binding of AbrB-like transcription factors.,Sullivan DM, Bobay BG, Kojetin DJ, Thompson RJ, Rance M, Strauch MA, Cavanagh J Structure. 2008 Nov 12;16(11):1702-13. PMID:19000822<ref>PMID:19000822</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_19000822}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2k1n" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 19000822 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19000822}}
+__TOC__
+</StructureSection>
-==About this Structure==
-K1N is a 6 chains structure of sequences from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K1N OCA].
-==Reference==
-Insights into the Nature of DNA Binding of AbrB-like Transcription Factors., Sullivan DM, Bobay BG, Kojetin DJ, Thompson RJ, Rance M, Strauch MA, Cavanagh J, Structure. 2008 Nov;16(11):1702-13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19000822 19000822]
 [[Category: Bacillus subtilis]]
-[[Category: Bobay, B G.]]
+[[Category: Large Structures]]
-[[Category: Cavanagh, J.]]
+[[Category: Synthetic construct]]
-[[Category: Sullivan, D M.]]
+[[Category: Bobay BG]]
-[[Category: Thompson, R J.]]
+[[Category: Cavanagh J]]
-[[Category: Abrb]]
+[[Category: Sullivan DM]]
-[[Category: Abrb8]]
+[[Category: Thompson RJ]]
-[[Category: Activator]]
-[[Category: Dna binding protein]]
-[[Category: Dna bound]]
-[[Category: Dna-binding]]
-[[Category: Repressor]]
-[[Category: Sporulation]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Transcription/dna complex]]
-[[Category: Transition state regulator]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 26 20:46:04 2008''