5j4i - Revision history

OCA at 10:48, 6 September 2023

OCA — Wed, 06 Sep 2023 10:48:06 GMT

←Older revision		Revision as of 10:48, 6 September 2023
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	<StructureSection load='5j4i' size='340' side='right'caption='[[5j4i]], [[Resolution\|resolution]] 2.21Å' scene=''>		<StructureSection load='5j4i' size='340' side='right'caption='[[5j4i]], [[Resolution\|resolution]] 2.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j4i]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Eco57 Eco57~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J4I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5J4I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j4i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J4I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J4I FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~adiC~~, ~~Z5717, ECs5097 (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=83334 ECO57])~~</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]] 2.207Å</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=5j4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j4i OCA], [~~http~~://pdbe.org/5j4i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5j4i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5j4i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5j4i 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=5j4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j4i OCA], [https://pdbe.org/5j4i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j4i RCSB], [https://www.ebi.ac.uk/pdbsum/5j4i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j4i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~ADIC_ECO57 ADIC_ECO57]~~] Major component of the acid-resistance (AR) system allowing enteric pathogens to survive the acidic environment in the stomach. Exchanges extracellular arginine for its intracellular decarboxylation product agmatine (Agm) thereby expelling intracellular protons.	+	[https://www.uniprot.org/uniprot/ADIC_ECOLI ADIC_ECOLI] Major component of the acid-resistance (AR) system allowing enteric pathogens to survive the acidic environment in the stomach (Probable). Exchanges extracellular arginine for its intracellular decarboxylation product agmatine (Agm) thereby expelling intracellular protons (PubMed:12867448, PubMed:14594828, PubMed:19578361, PubMed:21368142). Probably undergoes several conformational states in order to translocate the substrate across the membrane; keeps the substrate accessible to only 1 side of the membrane at a time by opening and closing 3 membrane-internal gates (Probable).<ref>PMID:12867448</ref> <ref>PMID:14594828</ref> <ref>PMID:19578361</ref> <ref>PMID:21368142</ref> <ref>PMID:14594828</ref> <ref>PMID:21368142</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: ~~Eco57~~]]	+	[[Category: Escherichia coli O157:H7]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fotiadis, D]]	+	[[Category: Fotiadis D]]
-	[[Category: Ilgue, H]]	+	[[Category: Ilgue H]]
-	[[Category: Jeckelmann~~, J M]]~~	+	[[Category: Jeckelmann JM]]
-	~~[[Category: Adic]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Transport protein]]~~	+
-	~~[[Category: Transporter~~]]	+

OCA at 07:28, 10 June 2020

OCA — Wed, 10 Jun 2020 07:28:58 GMT

←Older revision		Revision as of 07:28, 10 June 2020
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	==Crystal Structure of the L-arginine/agmatine antiporter from E. coli at 2.2 Angstroem resolution==		==Crystal Structure of the L-arginine/agmatine antiporter from E. coli at 2.2 Angstroem resolution==
-	<StructureSection load='5j4i' size='340' side='right' caption='[[5j4i]], [[Resolution\|resolution]] 2.21Å' scene=''>	+	<StructureSection load='5j4i' size='340' side='right'caption='[[5j4i]], [[Resolution\|resolution]] 2.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j4i]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J4I OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5J4I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j4i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Eco57 Eco57]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J4I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5J4I 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=5j4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j4i OCA], [http://pdbe.org/5j4i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j4i RCSB], [http://www.ebi.ac.uk/pdbsum/5j4i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j4i ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">adiC, Z5717, ECs5097 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57])</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=5j4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j4i OCA], [http://pdbe.org/5j4i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j4i RCSB], [http://www.ebi.ac.uk/pdbsum/5j4i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j4i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Eco57]]
		+	[[Category: Large Structures]]
	[[Category: Fotiadis, D]]		[[Category: Fotiadis, D]]
	[[Category: Ilgue, H]]		[[Category: Ilgue, H]]

OCA at 08:19, 14 September 2016

OCA — Wed, 14 Sep 2016 08:19:07 GMT

←Older revision		Revision as of 08:19, 14 September 2016
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/ADIC_ECO57 ADIC_ECO57]] Major component of the acid-resistance (AR) system allowing enteric pathogens to survive the acidic environment in the stomach. Exchanges extracellular arginine for its intracellular decarboxylation product agmatine (Agm) thereby expelling intracellular protons.		[[http://www.uniprot.org/uniprot/ADIC_ECO57 ADIC_ECO57]] Major component of the acid-resistance (AR) system allowing enteric pathogens to survive the acidic environment in the stomach. Exchanges extracellular arginine for its intracellular decarboxylation product agmatine (Agm) thereby expelling intracellular protons.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pathogenic enterobacteria need to survive the extreme acidity of the stomach to successfully colonize the human gut. Enteric bacteria circumvent the gastric acid barrier by activating extreme acid-resistance responses, such as the arginine-dependent acid resistance system. In this response, l-arginine is decarboxylated to agmatine, thereby consuming one proton from the cytoplasm. In Escherichia coli, the l-arginine/agmatine antiporter AdiC facilitates the export of agmatine in exchange of l-arginine, thus providing substrates for further removal of protons from the cytoplasm and balancing the intracellular pH. We have solved the crystal structures of wild-type AdiC in the presence and absence of the substrate agmatine at 2.6-A and 2.2-A resolution, respectively. The high-resolution structures made possible the identification of crucial water molecules in the substrate-binding sites, unveiling their functional roles for agmatine release and structure stabilization, which was further corroborated by molecular dynamics simulations. Structural analysis combined with site-directed mutagenesis and the scintillation proximity radioligand binding assay improved our understanding of substrate binding and specificity of the wild-type l-arginine/agmatine antiporter AdiC. Finally, we present a potential mechanism for conformational changes of the AdiC transport cycle involved in the release of agmatine into the periplasmic space of E. coli.
		+
		+	Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC.,Ilgu H, Jeckelmann JM, Gapsys V, Ucurum Z, de Groot BL, Fotiadis D Proc Natl Acad Sci U S A. 2016 Aug 31. pii: 201605442. PMID:27582465<ref>PMID:27582465</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5j4i" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:56, 10 September 2016

OCA — Sat, 10 Sep 2016 13:56:12 GMT

←Older revision		Revision as of 13:56, 10 September 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5j4i is ~~ON HOLD until Paper Publication~~	+	==Crystal Structure of the L-arginine/agmatine antiporter from E. coli at 2.2 Angstroem resolution==
-		+	<StructureSection load='5j4i' size='340' side='right' caption='[[5j4i]], [[Resolution\|resolution]] 2.21Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5j4i]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J4I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J4I 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=5j4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j4i OCA], [http://pdbe.org/5j4i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j4i RCSB], [http://www.ebi.ac.uk/pdbsum/5j4i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j4i ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ADIC_ECO57 ADIC_ECO57]] Major component of the acid-resistance (AR) system allowing enteric pathogens to survive the acidic environment in the stomach. Exchanges extracellular arginine for its intracellular decarboxylation product agmatine (Agm) thereby expelling intracellular protons.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Fotiadis, D]]
		+	[[Category: Ilgue, H]]
		+	[[Category: Jeckelmann, J M]]
		+	[[Category: Adic]]
		+	[[Category: Membrane protein]]
		+	[[Category: Transport protein]]
		+	[[Category: Transporter]]

OCA at 15:02, 15 May 2016

OCA — Sun, 15 May 2016 15:02:34 GMT

←Older revision		Revision as of 15:02, 15 May 2016
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	The entry 5j4i is ON HOLD until Paper Publication		The entry 5j4i is ON HOLD until Paper Publication

-	Authors: ~~Jeckelmann, J.M., Ilgue, H., Fotiadis, D.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Jeckelmann, J.M]]
-	[[Category: Fotiadis, D]]
-	[[Category: Ilgue, H]]

OCA: Protected "5j4i" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 01:26:50 GMT

Protected "5j4i" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:26, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5j4i is ON HOLD until Paper Publication Authors: Jeckelmann, J.M., Ilgue, H., Fotiadis, D. Description: Category: Unreleased Structures [[Cate...

OCA — Wed, 11 May 2016 01:26:48 GMT

New page: '''Unreleased structure''' The entry 5j4i is ON HOLD until Paper Publication Authors: Jeckelmann, J.M., Ilgue, H., Fotiadis, D. Description: Category: Unreleased Structures [[Cate...

New page

'''Unreleased structure'''

The entry 5j4i is ON HOLD until Paper Publication

Authors: Jeckelmann, J.M., Ilgue, H., Fotiadis, D.

Description:
[[Category: Unreleased Structures]]
[[Category: Jeckelmann, J.M]]
[[Category: Fotiadis, D]]
[[Category: Ilgue, H]]