5yil - Revision history

OCA at 08:30, 22 November 2023

2023-11-22T08:30:59Z

←Older revision		Revision as of 08:30, 22 November 2023
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	==Hoisting-loop in bacterial multidrug exporter AcrB is a highly flexible hinge that enables the large motion of the subdomains==		==Hoisting-loop in bacterial multidrug exporter AcrB is a highly flexible hinge that enables the large motion of the subdomains==
-	<StructureSection load='5yil' size='340' side='right' caption='[[5yil]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='5yil' size='340' side='right'caption='[[5yil]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yil]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YIL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yil]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YIL FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[3aoa\|3aoa]]</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]] 3Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">acrB, acrE, b0462, JW0451 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=83333 ECOLI])~~</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=5yil FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yil OCA], [https://pdbe.org/5yil PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yil RCSB], [https://www.ebi.ac.uk/pdbsum/5yil PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yil 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=5yil FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yil OCA], [~~http~~://pdbe.org/5yil PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yil RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yil PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yil ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ACRB_ECOLI ACRB_ECOLI]] AcrAB is a drug efflux protein with a broad substrate specificity.<ref>PMID:16915237</ref> <ref>PMID:16946072</ref> <ref>PMID:17194213</ref>	+	[https://www.uniprot.org/uniprot/ACRB_ECOLI ACRB_ECOLI] AcrAB is a drug efflux protein with a broad substrate specificity.<ref>PMID:16915237</ref> <ref>PMID:16946072</ref> <ref>PMID:17194213</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
-	[[Category: Hayashi, K]]	+	[[Category: Large Structures]]
-	[[Category: Kitagawa, K]]	+	[[Category: Hayashi K]]
-	[[Category: Nakashima, R]]	+	[[Category: Kitagawa K]]
-	[[Category: Nishino, K]]	+	[[Category: Nakashima R]]
-	[[Category: Sakurai, K]]	+	[[Category: Nishino K]]
-	[[Category: Yamaguchi, A]]	+	[[Category: Sakurai K]]
-	[[Category: Zwama, M]]	+	[[Category: Yamaguchi A]]
-	~~[[Category: Bacteria]]~~	+	[[Category: Zwama M]]
-	~~[[Category: Escherichia coli]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Multidrug efflux]]~~	+
-	~~[[Category: Rnd-type transporter]]~~	+
-	~~[[Category: Transport protein]]~~	+
-	~~[[Category: Transporter~~]]	+

OCA at 07:42, 29 November 2017

2017-11-29T07:42:17Z

←Older revision		Revision as of 07:42, 29 November 2017
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	<StructureSection load='5yil' size='340' side='right' caption='[[5yil]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='5yil' size='340' side='right' caption='[[5yil]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yil]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YIL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yil]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YIL FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3aoa\|3aoa]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3aoa\|3aoa]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">acrB, acrE, b0462, JW0451 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=5yil FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yil OCA], [http://pdbe.org/5yil PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yil RCSB], [http://www.ebi.ac.uk/pdbsum/5yil PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yil 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=5yil FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yil OCA], [http://pdbe.org/5yil PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yil RCSB], [http://www.ebi.ac.uk/pdbsum/5yil PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yil ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/ACRB_ECOLI ACRB_ECOLI]] AcrAB is a drug efflux protein with a broad substrate specificity.<ref>PMID:16915237</ref> <ref>PMID:16946072</ref> <ref>PMID:17194213</ref>		[[http://www.uniprot.org/uniprot/ACRB_ECOLI ACRB_ECOLI]] AcrAB is a drug efflux protein with a broad substrate specificity.<ref>PMID:16915237</ref> <ref>PMID:16946072</ref> <ref>PMID:17194213</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The overexpression of RND-type exporters is one of the main causes of multidrug resistance (MDR) in Gram-negative pathogens. In RND transporters, such as Escherichia coli's main efflux pump AcrB, drug efflux occurs in the porter domain, while protons flow through the transmembrane domain: remote conformational coupling. At the border of a transmembrane helix (TM8) and subdomain PC2, there is a loop which makes a hoisting movement by a random-coil-to-alpha-helix change, and opens and closes a drug channel entrance. This loop is supposed to play a key role in the allosteric conformational coupling between the transmembrane and porter domain. Here we show the results of a series of flexibility loop-mutants of AcrB. We determined the crystal structure of a three amino acid truncated loop mutant, which is still a functional transporter, and show that the short alpha-helix between Cbeta15 and the loop unwinds to a random coil in the access and binding monomers and in the extrusion monomer it makes a partially stretched coil-to-helix change. The loop has undergone compensatory conformational changes and still facilitates the opening and closing of the channel. In addition, more flexible mutated loops (proline mutated and significantly elongated) can still function during export. The flexibility in this region is however limited, as an even more truncated mutant (six amino acid deletion) becomes mostly inactive. We found that the hoisting-loop is a highly flexible hinge that enables the conformational energy transmission passively.
		+
		+	Hoisting-Loop in Bacterial Multidrug Exporter AcrB Is a Highly Flexible Hinge That Enables the Large Motion of the Subdomains.,Zwama M, Hayashi K, Sakurai K, Nakashima R, Kitagawa K, Nishino K, Yamaguchi A Front Microbiol. 2017 Oct 25;8:2095. doi: 10.3389/fmicb.2017.02095. eCollection, 2017. PMID:29118749<ref>PMID:29118749</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5yil" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
	[[Category: Hayashi, K]]		[[Category: Hayashi, K]]
	[[Category: Kitagawa, K]]		[[Category: Kitagawa, K]]

OCA at 07:39, 15 November 2017

2017-11-15T07:39:29Z

←Older revision		Revision as of 07:39, 15 November 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5yil is ~~ON HOLD~~	+	==Hoisting-loop in bacterial multidrug exporter AcrB is a highly flexible hinge that enables the large motion of the subdomains==
-		+	<StructureSection load='5yil' size='340' side='right' caption='[[5yil]], [[Resolution\|resolution]] 3.00Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5yil]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YIL FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3aoa\|3aoa]]</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=5yil FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yil OCA], [http://pdbe.org/5yil PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yil RCSB], [http://www.ebi.ac.uk/pdbsum/5yil PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yil ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ACRB_ECOLI ACRB_ECOLI]] AcrAB is a drug efflux protein with a broad substrate specificity.<ref>PMID:16915237</ref> <ref>PMID:16946072</ref> <ref>PMID:17194213</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hayashi, K]]
		+	[[Category: Kitagawa, K]]
		+	[[Category: Nakashima, R]]
		+	[[Category: Nishino, K]]
		+	[[Category: Sakurai, K]]
		+	[[Category: Yamaguchi, A]]
		+	[[Category: Zwama, M]]
		+	[[Category: Bacteria]]
		+	[[Category: Escherichia coli]]
		+	[[Category: Membrane protein]]
		+	[[Category: Multidrug efflux]]
		+	[[Category: Rnd-type transporter]]
		+	[[Category: Transport protein]]
		+	[[Category: Transporter]]

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

2017-10-11T05:25:12Z

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

←Older revision

Revision as of 05:25, 11 October 2017

OCA: New page: '''Unreleased structure''' The entry 5yil is ON HOLD Authors: Description: Category: Unreleased Structures

2017-10-11T05:25:11Z

New page: '''Unreleased structure''' The entry 5yil is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5yil is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]