5x13: Difference between revisions
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==Crystal structure of Bacillus subtilis PadR in complex with p-coumaric acid== | |||
<StructureSection load='5x13' size='340' side='right'caption='[[5x13]], [[Resolution|resolution]] 1.70Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5x13]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._spizizenii_str._W23 Bacillus subtilis subsp. spizizenii str. W23]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X13 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X13 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]] 1.7Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</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=5x13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x13 OCA], [https://pdbe.org/5x13 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x13 RCSB], [https://www.ebi.ac.uk/pdbsum/5x13 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x13 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/E0TW95_BACSH E0TW95_BACSH] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The PadR family is a large group of transcriptional regulators that function as environmental sensors. PadR negatively controls the expression of phenolic acid decarboxylase, which detoxifies harmful phenolic acids. To identify the mechanism by which PadR regulates phenolic acid-mediated gene expression, we performed structural and mutational studies of effector and operator recognition by Bacillus subtilis PadR. PadR contains an N-terminal winged helix-turn-helix (wHTH) domain (NTD) and a C-terminal homodimerization domain (CTD) and dimerizes into a dolmen shape. The PadR dimer interacts with the palindromic sequence of the operator DNA using the NTD. Two tyrosine residues and a positively charged residue in the NTD provide major DNA-binding energy and are highly conserved in the PadR family, suggesting that these three residues represent the canonical DNA-binding motif of the PadR family. PadR directly binds a phenolic acid effector molecule using a unique interdomain pocket created between the NTD and the CTD. Although the effector-binding site of PadR is positionally segregated from the DNA-binding site, effector binding to the interdomain pocket causes PadR to be rearranged into a DNA binding-incompatible conformer through an allosteric interdomain-reorganization mechanism. | |||
Structural basis of effector and operator recognition by the phenolic acid-responsive transcriptional regulator PadR.,Park SC, Kwak YM, Song WS, Hong M, Yoon SI Nucleic Acids Res. 2017 Nov 9. pii: 4607799. doi: 10.1093/nar/gkx1055. PMID:29136175<ref>PMID:29136175</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 5x13" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bacillus subtilis subsp. spizizenii str. W23]] | |||
[[Category: Large Structures]] | |||
[[Category: Hong M]] | |||
[[Category: Kwak YM]] | |||
[[Category: Park SC]] | |||
[[Category: Song WS]] | |||
[[Category: Yoon SI]] | |||
Latest revision as of 07:52, 22 November 2023
Crystal structure of Bacillus subtilis PadR in complex with p-coumaric acid
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