6ye6 - Revision history

OCA at 07:50, 7 February 2024

OCA — Wed, 07 Feb 2024 07:50:37 GMT

←Older revision		Revision as of 07:50, 7 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ye6]] is a 2 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=6YE6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YE6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ye6]] is a 2 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=6YE6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YE6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AG2:AGMATINE'>AG2</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=JFN:(2R)-1-methoxypropan-2-amine'>JFN</scene>, <scene name='pdbligand=ONT:(2~{S})-1-(2-methoxyethoxy)propan-2-amine'>ONT</scene>, <scene name='pdbligand=ONW:(2~{R})-1-[(2~{R})-1-(2-methoxyethoxy)propan-2-yl]oxypropan-2-amine'>ONW</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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]] 1.56Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AG2:AGMATINE'>AG2</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=JFN:(2R)-1-methoxypropan-2-amine'>JFN</scene>, <scene name='pdbligand=ONT:(2~{S})-1-(2-methoxyethoxy)propan-2-amine'>ONT</scene>, <scene name='pdbligand=ONW:(2~{R})-1-[(2~{R})-1-(2-methoxyethoxy)propan-2-yl]oxypropan-2-amine'>ONW</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=6ye6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ye6 OCA], [https://pdbe.org/6ye6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ye6 RCSB], [https://www.ebi.ac.uk/pdbsum/6ye6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ye6 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=6ye6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ye6 OCA], [https://pdbe.org/6ye6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ye6 RCSB], [https://www.ebi.ac.uk/pdbsum/6ye6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ye6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/POTF_ECOLI POTF_ECOLI] Required for the activity of the bacterial periplasmic transport system of putrescine. Polyamine binding protein.		[https://www.uniprot.org/uniprot/POTF_ECOLI POTF_ECOLI] Required for the activity of the bacterial periplasmic transport system of putrescine. Polyamine binding protein.
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Periplasmic binding proteins (PBPs) are ubiquitous receptors in gram-negative bacteria. They sense solutes and play key roles in nutrient uptake. Escherichia coli's putrescine receptor PotF has been reported to bind putrescine and spermidine. We reveal that several similar biogenic polyamines are recognized by PotF. Using isothermal titration calorimetry paired with X-ray crystallography of the different complexes, we unveil PotF's binding modes in detail. The binding site for PBPs is located between two lobes that undergo a large conformational change upon ligand recognition. Hence, analyzing the influence of ligands on complex formation is crucial. Therefore, we solved crystal structures of an open and closed apo state and used them as a basis for molecular dynamics simulations. In addition, we accessed structural behavior in solution for all complexes by (1)H-(15)N HSQC NMR spectroscopy. This combined analysis provides a robust framework for understanding ligand binding for future developments in drug design and protein engineering.
-
-	A comprehensive binding study illustrates ligand recognition in the periplasmic binding protein PotF.,Kroger P, Shanmugaratnam S, Ferruz N, Schweimer K, Hocker B Structure. 2020 Dec 30. pii: S0969-2126(20)30472-X. doi:, 10.1016/j.str.2020.12.005. PMID:33406388<ref>PMID:33406388</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6ye6" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 09:58, 15 March 2023

OCA — Wed, 15 Mar 2023 09:58:25 GMT

←Older revision		Revision as of 09:58, 15 March 2023
Line 3:		Line 3:
	<StructureSection load='6ye6' size='340' side='right'caption='[[6ye6]], [[Resolution\|resolution]] 1.56Å' scene=''>		<StructureSection load='6ye6' size='340' side='right'caption='[[6ye6]], [[Resolution\|resolution]] 1.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ye6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YE6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YE6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ye6]] is a 2 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=6YE6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YE6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AG2:AGMATINE'>AG2</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=JFN:(2R)-1-methoxypropan-2-amine'>JFN</scene>, <scene name='pdbligand=ONT:(2~{S})-1-(2-methoxyethoxy)propan-2-amine'>ONT</scene>, <scene name='pdbligand=ONW:(2~{R})-1-[(2~{R})-1-(2-methoxyethoxy)propan-2-yl]oxypropan-2-amine'>ONW</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AG2:AGMATINE'>AG2</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=JFN:(2R)-1-methoxypropan-2-amine'>JFN</scene>, <scene name='pdbligand=ONT:(2~{S})-1-(2-methoxyethoxy)propan-2-amine'>ONT</scene>, <scene name='pdbligand=ONW:(2~{R})-1-[(2~{R})-1-(2-methoxyethoxy)propan-2-yl]oxypropan-2-amine'>ONW</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6ye0\|6ye0]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">potF, b0854, JW0838 ([https://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=6ye6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ye6 OCA], [https://pdbe.org/6ye6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ye6 RCSB], [https://www.ebi.ac.uk/pdbsum/6ye6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ye6 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=6ye6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ye6 OCA], [https://pdbe.org/6ye6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ye6 RCSB], [https://www.ebi.ac.uk/pdbsum/6ye6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ye6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/POTF_ECOLI POTF_ECOLI]] Required for the activity of the bacterial periplasmic transport system of putrescine. Polyamine binding protein.	+	[https://www.uniprot.org/uniprot/POTF_ECOLI POTF_ECOLI] Required for the activity of the bacterial periplasmic transport system of putrescine. Polyamine binding protein.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hocker, B]]	+	[[Category: Hocker B]]
-	[[Category: Kroeger, P]]	+	[[Category: Kroeger P]]
-	[[Category: Shanmugaratnam, S]]	+	[[Category: Shanmugaratnam S]]
-	~~[[Category: Agmatine]]~~	+
-	~~[[Category: E coli]]~~	+
-	~~[[Category: Periplasmic binding protein]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 10:16, 19 May 2021

OCA — Wed, 19 May 2021 10:16:14 GMT

←Older revision		Revision as of 10:16, 19 May 2021
Line 1:		Line 1:

	==E.coli's Putrescine receptor PotF complexed with Agmatine==		==E.coli's Putrescine receptor PotF complexed with Agmatine==
-	<StructureSection load='6ye6' size='340' side='right'caption='[[6ye6]]' scene=''>	+	<StructureSection load='6ye6' size='340' side='right'caption='[[6ye6]], [[Resolution\|resolution]] 1.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YE6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6YE6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ye6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YE6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YE6 FirstGlance]. <br>
-	</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=6ye6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ye6 OCA], [~~http~~://pdbe.org/6ye6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ye6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ye6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ye6 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AG2:AGMATINE'>AG2</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=JFN:(2R)-1-methoxypropan-2-amine'>JFN</scene>, <scene name='pdbligand=ONT:(2~{S})-1-(2-methoxyethoxy)propan-2-amine'>ONT</scene>, <scene name='pdbligand=ONW:(2~{R})-1-[(2~{R})-1-(2-methoxyethoxy)propan-2-yl]oxypropan-2-amine'>ONW</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6ye0\|6ye0]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">potF, b0854, JW0838 ([https://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=6ye6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ye6 OCA], [https://pdbe.org/6ye6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ye6 RCSB], [https://www.ebi.ac.uk/pdbsum/6ye6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ye6 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/POTF_ECOLI POTF_ECOLI]] Required for the activity of the bacterial periplasmic transport system of putrescine. Polyamine binding protein.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Periplasmic binding proteins (PBPs) are ubiquitous receptors in gram-negative bacteria. They sense solutes and play key roles in nutrient uptake. Escherichia coli's putrescine receptor PotF has been reported to bind putrescine and spermidine. We reveal that several similar biogenic polyamines are recognized by PotF. Using isothermal titration calorimetry paired with X-ray crystallography of the different complexes, we unveil PotF's binding modes in detail. The binding site for PBPs is located between two lobes that undergo a large conformational change upon ligand recognition. Hence, analyzing the influence of ligands on complex formation is crucial. Therefore, we solved crystal structures of an open and closed apo state and used them as a basis for molecular dynamics simulations. In addition, we accessed structural behavior in solution for all complexes by (1)H-(15)N HSQC NMR spectroscopy. This combined analysis provides a robust framework for understanding ligand binding for future developments in drug design and protein engineering.
		+
		+	A comprehensive binding study illustrates ligand recognition in the periplasmic binding protein PotF.,Kroger P, Shanmugaratnam S, Ferruz N, Schweimer K, Hocker B Structure. 2020 Dec 30. pii: S0969-2126(20)30472-X. doi:, 10.1016/j.str.2020.12.005. PMID:33406388<ref>PMID:33406388</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ye6" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hocker B]]	+	[[Category: Hocker, B]]
-	[[Category: Kroeger P]]	+	[[Category: Kroeger, P]]
-	[[Category: Shanmugaratnam S]]	+	[[Category: Shanmugaratnam, S]]
		+	[[Category: Agmatine]]
		+	[[Category: E coli]]
		+	[[Category: Periplasmic binding protein]]
		+	[[Category: Transport protein]]

OCA at 08:12, 20 January 2021

OCA — Wed, 20 Jan 2021 08:12:00 GMT

←Older revision		Revision as of 08:12, 20 January 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ye6 is ~~ON HOLD until Paper Publication~~	+	==E.coli's Putrescine receptor PotF complexed with Agmatine==
-		+	<StructureSection load='6ye6' size='340' side='right'caption='[[6ye6]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YE6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YE6 FirstGlance]. <br>
-	~~Description~~:	+	</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=6ye6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ye6 OCA], [http://pdbe.org/6ye6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ye6 RCSB], [http://www.ebi.ac.uk/pdbsum/6ye6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ye6 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Hocker B]]
		+	[[Category: Kroeger P]]
		+	[[Category: Shanmugaratnam S]]

OCA at 07:18, 22 July 2020

OCA — Wed, 22 Jul 2020 07:18:57 GMT

←Older revision		Revision as of 07:18, 22 July 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ye6 is ON HOLD	+	The entry 6ye6 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6ye6" [edit=sysop:move=sysop]

OCA — Wed, 01 Apr 2020 07:43:51 GMT

Protected "6ye6" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:43, 1 April 2020

OCA: New page: '''Unreleased structure''' The entry 6ye6 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 01 Apr 2020 07:43:50 GMT

New page: '''Unreleased structure''' The entry 6ye6 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6ye6 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]