5x5j - Revision history

OCA at 10:17, 27 March 2024

OCA — Wed, 27 Mar 2024 10:17:20 GMT

←Older revision		Revision as of 10:17, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5x5j' size='340' side='right'caption='[[5x5j]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='5x5j' size='340' side='right'caption='[[5x5j]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x5j]] is a 1 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=5X5J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5X5J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x5j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X5J FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">[[~~5x5l~~\|~~5x5l~~]]</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]] 1.401Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5x5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5j OCA], [~~http~~://pdbe.org/5x5j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x5j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x5j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5j 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=5x5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5j OCA], [https://pdbe.org/5x5j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x5j RCSB], [https://www.ebi.ac.uk/pdbsum/5x5j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5j ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q6TA00_ACIBA Q6TA00_ACIBA]
-	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 5x5j" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aciba~~]]	+	[[Category: Acinetobacter baumannii]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Wen, Y]]	+	[[Category: Wen Y]]
-	~~[[Category: Ader]]~~	+
-	~~[[Category: Bacterial signaling transduction]]~~	+
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Response regulator]]~~	+
-	~~[[Category: Two-component regulatory system~~]]	+

OCA at 07:27, 7 October 2020

OCA — Wed, 07 Oct 2020 07:27:00 GMT

←Older revision		Revision as of 07:27, 7 October 2020
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	==Crystal structure of response regulator AdeR receiver domain==		==Crystal structure of response regulator AdeR receiver domain==
-	<StructureSection load='5x5j' size='340' side='right' caption='[[5x5j]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='5x5j' size='340' side='right'caption='[[5x5j]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x5j]] is a 1 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=5X5J OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X5J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x5j]] is a 1 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=5X5J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5X5J FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x5l\|5x5l]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x5l\|5x5l]]</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=5x5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5j OCA], [http://pdbe.org/5x5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x5j RCSB], [http://www.ebi.ac.uk/pdbsum/5x5j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5j ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5x5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5j OCA], [http://pdbe.org/5x5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x5j RCSB], [http://www.ebi.ac.uk/pdbsum/5x5j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5j ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Aciba]]		[[Category: Aciba]]
		+	[[Category: Large Structures]]
	[[Category: Wen, Y]]		[[Category: Wen, Y]]
	[[Category: Ader]]		[[Category: Ader]]

OCA at 07:36, 13 December 2017

OCA — Wed, 13 Dec 2017 07:36:13 GMT

←Older revision		Revision as of 07:36, 13 December 2017
Line 3:		Line 3:
	<StructureSection load='5x5j' size='340' side='right' caption='[[5x5j]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='5x5j' size='340' side='right' caption='[[5x5j]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x5j]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X5J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x5j]] is a 1 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=5X5J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X5J FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x5l\|5x5l]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x5l\|5x5l]]</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=5x5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5j OCA], [http://pdbe.org/5x5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x5j RCSB], [http://www.ebi.ac.uk/pdbsum/5x5j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5j 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=5x5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5j OCA], [http://pdbe.org/5x5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x5j RCSB], [http://www.ebi.ac.uk/pdbsum/5x5j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5j 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 5x5j" 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 14:37, 5 September 2017

OCA — Tue, 05 Sep 2017 14:37:59 GMT

←Older revision		Revision as of 14:37, 5 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5x5j is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of response regulator AdeR receiver domain==
-		+	<StructureSection load='5x5j' size='340' side='right' caption='[[5x5j]], [[Resolution\|resolution]] 1.40Å' scene=''>
-	~~Authors~~: ~~Yurong~~, W.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5x5j]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X5J FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of response regulator AdeR receiver domain~~	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x5l\|5x5l]]</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=5x5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5j OCA], [http://pdbe.org/5x5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x5j RCSB], [http://www.ebi.ac.uk/pdbsum/5x5j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5j ProSAT]</span></td></tr>
-	[[Category: ~~Yurong, W~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Wen, Y]]
		+	[[Category: Ader]]
		+	[[Category: Bacterial signaling transduction]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Response regulator]]
		+	[[Category: Two-component regulatory system]]

OCA at 12:16, 5 April 2017

OCA — Wed, 05 Apr 2017 12:16:54 GMT

←Older revision		Revision as of 12:16, 5 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5x5j is ON HOLD	+	The entry 5x5j is ON HOLD until Paper Publication

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

OCA: Protected "5x5j" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 15:46:43 GMT

Protected "5x5j" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:46, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5x5j is ON HOLD Authors: Yurong, W. Description: Crystal structure of response regulator AdeR receiver domain Category: Unreleased Structures [...

OCA — Thu, 09 Mar 2017 15:46:42 GMT

New page: '''Unreleased structure''' The entry 5x5j is ON HOLD Authors: Yurong, W. Description: Crystal structure of response regulator AdeR receiver domain Category: Unreleased Structures [...

New page

'''Unreleased structure'''

The entry 5x5j is ON HOLD

Authors: Yurong, W.

Description: Crystal structure of response regulator AdeR receiver domain
[[Category: Unreleased Structures]]
[[Category: Yurong, W]]