1yfb: Difference between revisions

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-{{Seed}}
-[[Image:1yfb.png|left|200px]]
-<!--
+==The solution structure of the N-domain of the transcription factor abrB==
-The line below this paragraph, containing "STRUCTURE_1yfb", creates the "Structure Box" on the page.
+<StructureSection load='1yfb' size='340' side='right'caption='[[1yfb]]' 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'>[[1yfb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YFB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YFB 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</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=1yfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yfb OCA], [https://pdbe.org/1yfb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yfb RCSB], [https://www.ebi.ac.uk/pdbsum/1yfb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yfb ProSAT]</span></td></tr>
-{{STRUCTURE_1yfb|  PDB=1yfb  |  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/yf/1yfb_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=1yfb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+AbrB is a key transition-state regulator of Bacillus subtilis. Based on the conservation of a betaalphabeta structural unit, we proposed a beta barrel fold for its DNA binding domain, similar to, but topologically distinct from, double-psi beta barrels. However, the NMR structure revealed a novel fold, the "looped-hinge helix." To understand this discrepancy, we undertook a bioinformatics study of AbrB and its homologs; these form a large superfamily, which includes SpoVT, PrlF, MraZ, addiction module antidotes (PemI, MazE), plasmid maintenance proteins (VagC, VapB), and archaeal PhoU homologs. MazE and MraZ form swapped-hairpin beta barrels. We therefore reexamined the fold of AbrB by NMR spectroscopy and found that it also forms a swapped-hairpin barrel. The conservation of the core betaalphabeta element supports a common evolutionary origin for swapped-hairpin and double-psi barrels, which we group into a higher-order class, the cradle-loop barrels, based on the peculiar shape of their ligand binding site.
-===The solution structure of the N-domain of the transcription factor abrB===
+AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels.,Coles M, Djuranovic S, Soding J, Frickey T, Koretke K, Truffault V, Martin J, Lupas AN Structure. 2005 Jun;13(6):919-28. PMID:15939023<ref>PMID:15939023</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_15939023}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1yfb" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 15939023 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15939023}}
+__TOC__
+</StructureSection>
-==About this Structure==
-YFB is a [[Single protein]] structure of sequence 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=1YFB OCA].
-==Reference==
-AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels., Coles M, Djuranovic S, Soding J, Frickey T, Koretke K, Truffault V, Martin J, Lupas AN, Structure. 2005 Jun;13(6):919-28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15939023 15939023]
 [[Category: Bacillus subtilis]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Coles, M.]]
+[[Category: Coles M]]
-[[Category: Djuranovic, S.]]
+[[Category: Djuranovic S]]
-[[Category: Truffault, V.]]
+[[Category: Truffault V]]
-[[Category: Bioinformatic]]
-[[Category: Homodimer]]
-[[Category: Nmr]]
-[[Category: Swapped-hairpin barrel]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 15:39:39 2008''