2p5l: Difference between revisions
New page: left|200px<br /><applet load="2p5l" size="350" color="white" frame="true" align="right" spinBox="true" caption="2p5l, resolution 2.85Å" /> '''Crystal structure of... |
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== | ==Crystal structure of a dimer of N-terminal domains of AhrC in complex with an 18bp DNA operator site== | ||
<StructureSection load='2p5l' size='340' side='right'caption='[[2p5l]], [[Resolution|resolution]] 2.85Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2p5l]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P5L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P5L 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]] 2.85Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2p5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p5l OCA], [https://pdbe.org/2p5l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p5l RCSB], [https://www.ebi.ac.uk/pdbsum/2p5l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p5l ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/ARGR_BACSU ARGR_BACSU] Represses the synthesis of biosynthetic enzymes and activates the arginine catabolism. Controls the transcription of the two operons rocABC and rocDEF. | |||
== 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/p5/2p5l_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=2p5l ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
In many bacteria, the concentration of L-arginine is controlled by a transcriptional regulator, the arginine repressor. In Bacillus subtilis this transcription factor is called AhrC and has roles in both the repression and activation of the genes involved in arginine metabolism. It interacts with 18 bp ARG boxes in the promoters of arginine biosynthetic and catabolic operons. AhrC is a hexamer and each subunit has two domains. The C-terminal domains form the core, mediating inter-subunit interactions and L-arginine binding, while the N-terminal domains contain a winged helix-turn-helix DNA-binding motif and are arranged around the periphery. Upon binding of the co-repressor L-arginine there is a approximately 15 degrees relative rotation between core C-terminal trimers. Here, we report the X-ray crystal structure of a dimer of the N-terminal domains of AhrC (NAhrC) in complex with an 18 bp DNA ARG box operator, refined to 2.85 A resolution. Comparison of the N-terminal domains within this complex with those of the free domain reveals that the flexible beta-wings of the DNA-binding motif in the free domain form a stable dimer interface in the protein-DNA complex, favouring correct orientation of the recognition helices. These are then positioned to insert into adjacent turns of the major groove of the ARG box, whilst the wings contact the minor groove. There are extensive contacts between the protein and the DNA phosphodiester backbone, as well as a number of direct hydrogen bonds between conserved amino acid side chains and bases. Combining this structure with other crystal structures of other AhrC components, we have constructed a model of the repression complex of AhrC at the B. subtilis biosynthetic argC operator and, along with transcriptome data, analysed the origins of sequence specificity and arginine activation. | |||
Structure and function of the arginine repressor-operator complex from Bacillus subtilis.,Garnett JA, Marincs F, Baumberg S, Stockley PG, Phillips SE J Mol Biol. 2008 May 30;379(2):284-98. Epub 2008 Mar 12. PMID:18455186<ref>PMID:18455186</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2p5l" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Arginine repressor 3D structures|Arginine repressor 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bacillus subtilis]] | [[Category: Bacillus subtilis]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Baumberg | [[Category: Baumberg S]] | ||
[[Category: Garnett | [[Category: Garnett JA]] | ||
[[Category: Marincs | [[Category: Marincs F]] | ||
[[Category: Phillips | [[Category: Phillips SEV]] | ||
[[Category: Stockley | [[Category: Stockley PG]] | ||
