5y8t - Revision history

OCA at 08:24, 22 November 2023

OCA — Wed, 22 Nov 2023 08:24:40 GMT

←Older revision		Revision as of 08:24, 22 November 2023
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	==Crystal structure of Bacillus subtilis PadR in complex with p-coumaric acid==		==Crystal structure of Bacillus subtilis PadR in complex with p-coumaric acid==
-	<StructureSection load='5y8t' size='340' side='right' caption='[[5y8t]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5y8t' size='340' side='right'caption='[[5y8t]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y8t]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacpz Bacpz~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y8T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Y8T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y8t]] is a 3 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=5Y8T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y8T FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=HC4:4~~-~~HYDROXYCINNAMIC+ACID'>HC4</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~padR, BSUW23_04210 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=655816 BACPZ])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5y8t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y8t OCA], [~~http~~://pdbe.org/5y8t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5y8t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5y8t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5y8t ProSAT]</span></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=5y8t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y8t OCA], [https://pdbe.org/5y8t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y8t RCSB], [https://www.ebi.ac.uk/pdbsum/5y8t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y8t ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/E0TW95_BACSH E0TW95_BACSH]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5y8t" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5y8t" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Transcriptional activator 3D structures\|Transcriptional activator 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacpz~~]]	+	[[Category: Bacillus subtilis subsp. spizizenii str. W23]]
-	[[Category: ~~Hong, M~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kwak, Y~~ M]]	+	[[Category: Hong M]]
-	[[Category: ~~Park, S C~~]]	+	[[Category: Kwak YM]]
-	[[Category: ~~Song, W S~~]]	+	[[Category: Park SC]]
-	[[Category: ~~Yoon, S I~~]]	+	[[Category: Song WS]]
-	[[Category: ~~Transcription]]~~	+	[[Category: Yoon SI]]
-	~~[[Category: Transcription factor~~]]	+

OCA at 08:58, 27 December 2017

OCA — Wed, 27 Dec 2017 08:58:30 GMT

←Older revision		Revision as of 08:58, 27 December 2017
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	<StructureSection load='5y8t' size='340' side='right' caption='[[5y8t]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5y8t' size='340' side='right' caption='[[5y8t]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y8t]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y8T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y8T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y8t]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacpz Bacpz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y8T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y8T FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">padR, BSUW23_04210 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=655816 BACPZ])</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5y8t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y8t OCA], [http://pdbe.org/5y8t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y8t RCSB], [http://www.ebi.ac.uk/pdbsum/5y8t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y8t ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5y8t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y8t OCA], [http://pdbe.org/5y8t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y8t RCSB], [http://www.ebi.ac.uk/pdbsum/5y8t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y8t ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacpz]]
	[[Category: Hong, M]]		[[Category: Hong, M]]
	[[Category: Kwak, Y M]]		[[Category: Kwak, Y M]]

OCA at 06:13, 29 November 2017

OCA — Wed, 29 Nov 2017 06:13:57 GMT

←Older revision		Revision as of 06:13, 29 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5y8t is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Bacillus subtilis PadR in complex with p-coumaric acid==
		+	<StructureSection load='5y8t' size='340' side='right' caption='[[5y8t]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5y8t]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y8T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y8T FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5y8t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y8t OCA], [http://pdbe.org/5y8t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y8t RCSB], [http://www.ebi.ac.uk/pdbsum/5y8t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y8t ProSAT]</span></td></tr>
		+	</table>
		+	<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.

-	~~Authors~~:	+	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>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5y8t" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hong, M]]
		+	[[Category: Kwak, Y M]]
		+	[[Category: Park, S C]]
		+	[[Category: Song, W S]]
		+	[[Category: Yoon, S I]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription factor]]

OCA: Protected "5y8t" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 16:16:43 GMT

Protected "5y8t" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:16, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5y8t is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 16:16:42 GMT

New page: '''Unreleased structure''' The entry 5y8t is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5y8t is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]