5xxp - Revision history

OCA at 08:17, 22 November 2023

OCA — Wed, 22 Nov 2023 08:17:15 GMT

←Older revision		Revision as of 08:17, 22 November 2023
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	==Crystal structure of CbnR_DBD-DNA complex==		==Crystal structure of CbnR_DBD-DNA complex==
-	<StructureSection load='5xxp' size='340' side='right' caption='[[5xxp]], [[Resolution\|resolution]] 2.55Å' scene=''>	+	<StructureSection load='5xxp' size='340' side='right'caption='[[5xxp]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xxp]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_17697_[[alcaligenes_eutrophus]] Atcc 17697 [[alcaligenes eutrophus]]~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XXP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XXP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xxp]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Cupriavidus_necator Cupriavidus necator]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XXP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XXP FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~cbnR~~, ~~BJN34_37375 (~~[~~http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=106590 ATCC 17697~~ [~~[Alcaligenes eutrophus~~]]])</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]] 2.55Å</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=5xxp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xxp OCA], [~~http~~://pdbe.org/5xxp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xxp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xxp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xxp 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=5xxp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xxp OCA], [https://pdbe.org/5xxp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xxp RCSB], [https://www.ebi.ac.uk/pdbsum/5xxp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xxp ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9WXC7_CUPNE Q9WXC7_CUPNE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5xxp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5xxp" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Transcriptional activator 3D structures\|Transcriptional activator 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Senda, M~~]]	+	[[Category: Cupriavidus necator]]
-	[[Category: ~~Senda, T~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Dna binding domain~~]]	+	[[Category: Senda M]]
-	[[Category: ~~Dna binding protein]]~~	+	[[Category: Senda T]]
-	~~[[Category: Dna complex~~]]	+

OCA at 06:46, 7 February 2018

OCA — Wed, 07 Feb 2018 06:46:20 GMT

←Older revision		Revision as of 06:46, 7 February 2018
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	<StructureSection load='5xxp' size='340' side='right' caption='[[5xxp]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='5xxp' size='340' side='right' caption='[[5xxp]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xxp]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XXP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XXP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xxp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_17697_[[alcaligenes_eutrophus]] Atcc 17697 [[alcaligenes eutrophus]]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XXP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XXP FirstGlance]. <br>
-	</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=5xxp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xxp OCA], [http://pdbe.org/5xxp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xxp RCSB], [http://www.ebi.ac.uk/pdbsum/5xxp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xxp ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbnR, BJN34_37375 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=106590 ATCC 17697 [[Alcaligenes eutrophus]]])</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=5xxp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xxp OCA], [http://pdbe.org/5xxp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xxp RCSB], [http://www.ebi.ac.uk/pdbsum/5xxp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xxp ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	LysR-type transcriptional regulators (LTTRs) are among the most abundant transcriptional regulators in bacteria. CbnR is an LTTR derived from Cupriavidus necator (formerly Alcaligenes eutrophus or Ralstonia eutropha) NH9 and is involved in transcriptional activation of the cbnABCD genes encoding chlorocatechol degradative enzymes. CbnR interacts with a cbnA promoter region of approximately 60 bp in length that contains the recognition-binding site (RBS) and activation-binding site (ABS). Upon inducer binding, CbnR seems to undergo conformational changes, leading to the activation of the transcription. Since the interaction of an LTTR with RBS is considered to be the first step of the transcriptional activation, the CbnR-RBS interaction is responsible for the selectivity of the promoter to be activated. To understand the sequence selectivity of CbnR, we determined the crystal structure of the DNA-binding domain of CbnR in complex with RBS of the cbnA promoter at 2.55 A resolution. The crystal structure revealed details of the interactions between the DNA-binding domain and the promoter DNA. A comparison with the previously reported crystal structure of the DNA-binding domain of BenM in complex with its cognate RBS showed several differences in the DNA interactions, despite the structural similarity between CbnR and BenM. These differences explain the observed promoter sequence selectivity between CbnR and BenM. Particularly, the difference between Thr33 in CbnR and Ser33 in BenM appears to affect the conformations of neighboring residues, leading to the selective interactions with DNA. DATABASE: Atomic coordinates and structure factors for the DNA-binding domain of Cupriavidus necatorNH9 CbnR in complex with RBS are available in the Protein Data Bank under the accession code 5XXP.
		+
		+	Crystal structure of the DNA-binding domain of the LysR-type transcriptional regulator CbnR in complex with a DNA fragment of the recognition-binding site in the promoter region.,Koentjoro MP, Adachi N, Senda M, Ogawa N, Senda T FEBS J. 2018 Jan 11. doi: 10.1111/febs.14380. PMID:29323785<ref>PMID:29323785</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5xxp" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:57, 17 January 2018

OCA — Wed, 17 Jan 2018 06:57:19 GMT

←Older revision		Revision as of 06:57, 17 January 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5xxp is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of CbnR_DBD-DNA complex==
-		+	<StructureSection load='5xxp' size='340' side='right' caption='[[5xxp]], [[Resolution\|resolution]] 2.55Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5xxp]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XXP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XXP FirstGlance]. <br>
-	~~Description~~:	+	</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=5xxp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xxp OCA], [http://pdbe.org/5xxp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xxp RCSB], [http://www.ebi.ac.uk/pdbsum/5xxp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xxp ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Senda, M]]
		+	[[Category: Senda, T]]
		+	[[Category: Dna binding domain]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Dna complex]]

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

OCA — Wed, 27 Sep 2017 15:53:53 GMT

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

←Older revision

Revision as of 15:53, 27 September 2017

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

OCA — Wed, 27 Sep 2017 15:53:52 GMT

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

New page

'''Unreleased structure'''

The entry 5xxp is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]