5ito - Revision history

OCA at 14:09, 30 August 2023

2023-08-30T14:09:05Z

←Older revision		Revision as of 14:09, 30 August 2023
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	<StructureSection load='5ito' size='340' side='right'caption='[[5ito]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='5ito' size='340' side='right'caption='[[5ito]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ito]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Agrfc Agrfc~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ITO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ITO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ito]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_fabrum_str._C58 Agrobacterium fabrum str. C58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ITO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ITO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=6DB:OCTOPINE'>6DB</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TOE:2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL'>TOE</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]] 2.35Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4p0i\|4p0i]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=6DB:OCTOPINE'>6DB</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TOE:2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL'>TOE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nocT, Atu6027, AGR_pTi_67 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176299 AGRFC])</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=5ito FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ito OCA], [https://pdbe.org/5ito PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ito RCSB], [https://www.ebi.ac.uk/pdbsum/5ito PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ito 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=5ito FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ito OCA], [~~http~~://pdbe.org/5ito PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ito RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ito PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ito ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NOCT_AGRFC NOCT_AGRFC]] Component of the nopaline active transport system probably consisting of four subunits: Q, M, P and T. This system is also capable of transporting octopine provided that catabolic functions are induced with nopaline.	+	[https://www.uniprot.org/uniprot/NOCT_AGRFC NOCT_AGRFC] Component of the nopaline active transport system probably consisting of four subunits: Q, M, P and T. This system is also capable of transporting octopine provided that catabolic functions are induced with nopaline.
	<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: ~~Agrfc~~]]	+	[[Category: Agrobacterium fabrum str. C58]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Morera, S]]	+	[[Category: Morera S]]
-	[[Category: Vigouroux, A]]	+	[[Category: Vigouroux A]]
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Octopine]]~~	+
-	~~[[Category: Opine]]~~	+
-	~~[[Category: Periplasmic binding protein~~]]	+

OCA at 07:31, 3 June 2020

2020-06-03T07:31:24Z

←Older revision		Revision as of 07:31, 3 June 2020
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	==Structure of the periplasmic binding protein M117N-NocT from A. tumefaciens in complex with octopine==		==Structure of the periplasmic binding protein M117N-NocT from A. tumefaciens in complex with octopine==
-	<StructureSection load='5ito' size='340' side='right' caption='[[5ito]], [[Resolution\|resolution]] 2.35Å' scene=''>	+	<StructureSection load='5ito' size='340' side='right'caption='[[5ito]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ito]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ITO OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ITO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ito]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrfc Agrfc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ITO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ITO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=6DB:OCTOPINE'>6DB</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TOE:2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL'>TOE</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=6DB:OCTOPINE'>6DB</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TOE:2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL'>TOE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4p0i\|4p0i]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4p0i\|4p0i]]</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=5ito FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ito OCA], [http://pdbe.org/5ito PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ito RCSB], [http://www.ebi.ac.uk/pdbsum/5ito PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ito ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nocT, Atu6027, AGR_pTi_67 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176299 AGRFC])</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=5ito FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ito OCA], [http://pdbe.org/5ito PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ito RCSB], [http://www.ebi.ac.uk/pdbsum/5ito PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ito ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Agrfc]]
		+	[[Category: Large Structures]]
	[[Category: Morera, S]]		[[Category: Morera, S]]
	[[Category: Vigouroux, A]]		[[Category: Vigouroux, A]]

OCA at 18:33, 10 December 2016

2016-12-10T18:33:50Z

←Older revision		Revision as of 18:33, 10 December 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5ito is ~~ON HOLD until Paper~~ Publication	+	==Structure of the periplasmic binding protein M117N-NocT from A. tumefaciens in complex with octopine==
		+	<StructureSection load='5ito' size='340' side='right' caption='[[5ito]], [[Resolution\|resolution]] 2.35Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ito]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ITO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ITO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=6DB:OCTOPINE'>6DB</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TOE:2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL'>TOE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4p0i\|4p0i]]</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=5ito FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ito OCA], [http://pdbe.org/5ito PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ito RCSB], [http://www.ebi.ac.uk/pdbsum/5ito PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ito ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NOCT_AGRFC NOCT_AGRFC]] Component of the nopaline active transport system probably consisting of four subunits: Q, M, P and T. This system is also capable of transporting octopine provided that catabolic functions are induced with nopaline.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We investigated the molecular and ecological mechanisms involved in niche expansion, or generalism, versus specialization in sympatric plant pathogens. Nopaline-type and octopine-type Agrobacterium tumefaciens engineer distinct niches in their plant hosts that provide different nutrients: nopaline or octopine, respectively. Previous studies revealed that nopaline-type pathogens may expand their niche to also assimilate octopine in the presence of nopaline, but consequences of this phenomenon on pathogen dynamics in planta were not known. Here, we provided molecular insight into how the transport protein NocT can bind octopine as well as nopaline, contributing to niche expansion. We further showed that despite the ability for niche expansion, nopaline-type pathogens had no competitive advantage over octopine-type pathogens in co-infected plants. We also demonstrated that a single nucleotide polymorphism in the nocR gene was sufficient to allow octopine assimilation by nopaline-type strains even in absence of nopaline. The evolved nocR bacteria had higher fitness than their ancestor in octopine-rich transgenic plants but lower fitness in tumors induced by octopine-type pathogens. Overall, this work elucidates the specialization of A. tumefaciens to particular opine niches and explains why generalists do not always spread despite the advantage associated with broader nutritional niches.The ISME Journal advance online publication, 1 November 2016; doi:10.1038/ismej.2016.137.

-	~~Authors~~:	+	Fitness costs restrict niche expansion by generalist niche-constructing pathogens.,Lang J, Vigouroux A, El Sahili A, Kwasiborski A, Aumont-Nicaise M, Dessaux Y, Shykoff JA, Morera S, Faure D ISME J. 2016 Nov 1. doi: 10.1038/ismej.2016.137. PMID:27801902<ref>PMID:27801902</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5ito" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Morera, S]]
		+	[[Category: Vigouroux, A]]
		+	[[Category: Membrane protein]]
		+	[[Category: Octopine]]
		+	[[Category: Opine]]
		+	[[Category: Periplasmic binding protein]]

OCA at 14:43, 15 May 2016

2016-05-15T14:43:49Z

←Older revision		Revision as of 14:43, 15 May 2016
Line 3:		Line 3:
	The entry 5ito is ON HOLD until Paper Publication		The entry 5ito is ON HOLD until Paper Publication

-	Authors: ~~Vigouroux, A., Morera, S.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Morera, S]]
-	[[Category: Vigouroux, A]]

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

2016-05-11T00:56:00Z

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

←Older revision

Revision as of 00:56, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5ito is ON HOLD until Paper Publication Authors: Vigouroux, A., Morera, S. Description: Category: Unreleased Structures [[Category: Morera, S]...

2016-05-11T00:55:59Z

New page: '''Unreleased structure''' The entry 5ito is ON HOLD until Paper Publication Authors: Vigouroux, A., Morera, S. Description: Category: Unreleased Structures [[Category: Morera, S]...

New page

'''Unreleased structure'''

The entry 5ito is ON HOLD until Paper Publication

Authors: Vigouroux, A., Morera, S.

Description:
[[Category: Unreleased Structures]]
[[Category: Morera, S]]
[[Category: Vigouroux, A]]