5x5l - Revision history

OCA at 07:54, 22 November 2023

2023-11-22T07:54:13Z

←Older revision		Revision as of 07:54, 22 November 2023
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	==Crystal structure of response regulator AdeR DNA binding domain in complex with an intercistronic region==		==Crystal structure of response regulator AdeR DNA binding domain in complex with an intercistronic region==
-	<StructureSection load='5x5l' size='340' side='right' caption='[[5x5l]], [[Resolution\|resolution]] 2.75Å' scene=''>	+	<StructureSection load='5x5l' size='340' side='right'caption='[[5x5l]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x5l]] is a 10 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aciba Aciba~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5L OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X5L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x5l]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X5L FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5x5j\|5x5j]]</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]] 2.75Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">adeR ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=470 ACIBA])~~</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=5x5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5l OCA], [https://pdbe.org/5x5l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x5l RCSB], [https://www.ebi.ac.uk/pdbsum/5x5l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5l 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=5x5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5l OCA], [~~http~~://pdbe.org/5x5l PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x5l RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x5l PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5l ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/E1A0Z5_ACIBA E1A0Z5_ACIBA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aciba~~]]	+	[[Category: Acinetobacter baumannii]]
-	[[Category: ~~Wen, Y~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Ader~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Bacterial signaling transduction]]~~	+	[[Category: Wen Y]]
-	~~[[Category: Dna binding protein-dna complex]]~~	+
-	~~[[Category: Response regulator]]~~	+
-	~~[[Category: Two-component regulatory system~~]]	+

OCA at 07:36, 13 December 2017

2017-12-13T07:36:16Z

←Older revision		Revision as of 07:36, 13 December 2017
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	<StructureSection load='5x5l' size='340' side='right' caption='[[5x5l]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='5x5l' size='340' side='right' caption='[[5x5l]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x5l]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X5L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x5l]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Aciba Aciba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X5L FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x5j\|5x5j]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x5j\|5x5j]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">adeR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=470 ACIBA])</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=5x5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5l OCA], [http://pdbe.org/5x5l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x5l RCSB], [http://www.ebi.ac.uk/pdbsum/5x5l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5l 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=5x5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5l OCA], [http://pdbe.org/5x5l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x5l RCSB], [http://www.ebi.ac.uk/pdbsum/5x5l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5l ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	AdeR-AdeS is a two-component regulatory system, which controls expression of the adeABC efflux pump involved in Acinetobacter baumannii multidrug resistance. AdeR is a response regulator consisting of an N-terminal receiver domain and a C-terminal DNA-binding-domain. AdeR binds to a direct-repeat DNA in the intercistronic region between adeR and adeABC. We demonstrate a markedly high affinity binding between unphosphorylated AdeR and DNA with a dissociation constant of 20 nM. In addition, we provide a 2.75 A crystal structure of AdeR DNA-binding-domain complexed with the intercistronic DNA. This structure shows that the alpha3 and beta hairpin formed by beta5-beta6 interacts with the major and minor groove of the DNA, which in turn leads to the introduction of a bend. The AdeR receiver domain structure revealed a dimerization motif mediated by a gearwheel-like structure involving the D108F109-R122 motif through cation pi stack interaction. The structure of AdeR receiver domain bound with magnesium indicated a conserved Glu19Asp20-Asp63 magnesium-binding motif, and revealed that the potential phosphorylation site Asp63OD1 forms a hydrogen bond with Lys112. We thus dissected the mechanism of how AdeR recognizes the intercistronic DNA, which leads to a diverse mode of response regulation. Unlocking the AdeRS mechanism provides ways to circumvent A. baumannii antibiotic resistance.
		+
		+	Mechanistic insight into how multidrug resistant Acinetobacter baumannii response regulator AdeR recognizes an intercistronic region.,Wen Y, Ouyang Z, Yu Y, Zhou X, Pei Y, Devreese B, Higgins PG, Zheng F Nucleic Acids Res. 2017 Sep 19;45(16):9773-9787. doi: 10.1093/nar/gkx624. PMID:28934482<ref>PMID:28934482</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5x5l" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aciba]]
	[[Category: Wen, Y]]		[[Category: Wen, Y]]
	[[Category: Ader]]		[[Category: Ader]]

OCA at 14:42, 5 September 2017

2017-09-05T14:42:11Z

←Older revision		Revision as of 14:42, 5 September 2017
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-	'''Unreleased structure'''

-	~~The entry 5x5l is ON HOLD until Paper Publication~~	+	==Crystal structure of response regulator AdeR DNA binding domain in complex with an intercistronic region==
-		+	<StructureSection load='5x5l' size='340' side='right' caption='[[5x5l]], [[Resolution\|resolution]] 2.75Å' scene=''>
-	~~Authors: Yurong, W.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5x5l]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X5L FirstGlance]. <br>
-	~~Description:~~ Crystal structure of response regulator AdeR DNA binding domain in complex with an intercistronic region	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x5j\|5x5j]]</td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5x5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5l OCA], [http://pdbe.org/5x5l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x5l RCSB], [http://www.ebi.ac.uk/pdbsum/5x5l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5l ProSAT]</span></td></tr>
-	[[Category: ~~Yurong~~, W]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Wen, Y]]
		+	[[Category: Ader]]
		+	[[Category: Bacterial signaling transduction]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Response regulator]]
		+	[[Category: Two-component regulatory system]]

OCA at 12:17, 5 April 2017

2017-04-05T12:17:00Z

←Older revision		Revision as of 12:17, 5 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5x5l is ON HOLD	+	The entry 5x5l is ON HOLD until Paper Publication

	Authors: Yurong, W.		Authors: Yurong, W.

OCA: Protected "5x5l" [edit=sysop:move=sysop]

2017-03-09T15:46:58Z

Protected "5x5l" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:46, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5x5l is ON HOLD Authors: Yurong, W. Description: Crystal structure of response regulator AdeR DNA binding domain in complex with an intercistronic ...

2017-03-09T15:46:56Z

New page: '''Unreleased structure''' The entry 5x5l is ON HOLD Authors: Yurong, W. Description: Crystal structure of response regulator AdeR DNA binding domain in complex with an intercistronic ...

New page

'''Unreleased structure'''

The entry 5x5l is ON HOLD

Authors: Yurong, W.

Description: Crystal structure of response regulator AdeR DNA binding domain in complex with an intercistronic region
[[Category: Unreleased Structures]]
[[Category: Yurong, W]]