5ore - Revision history

OCA at 16:58, 13 December 2023

2023-12-13T16:58:58Z

←Older revision		Revision as of 16:58, 13 December 2023
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	==Structure of the periplasmic binding protein (PBP) OccJ from agrobacterium tumefaciens B6==		==Structure of the periplasmic binding protein (PBP) OccJ from agrobacterium tumefaciens B6==
-	<StructureSection load='5ore' size='340' side='right' caption='[[5ore]], [[Resolution\|resolution]] 2.35Å' scene=''>	+	<StructureSection load='5ore' size='340' side='right'caption='[[5ore]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ore]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ORE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ORE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ore]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ORE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ORE FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CL:CHLORIDE+ION'>CL</scene~~>, ~~<scene name='pdbligand=EDO:1,~~2~~-ETHANEDIOL'>EDO</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='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~occT, occJ ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=358 "Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></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=5ore FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ore OCA], [~~http~~://pdbe.org/5ore PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ore RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ore PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ore 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=5ore FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ore OCA], [https://pdbe.org/5ore PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ore RCSB], [https://www.ebi.ac.uk/pdbsum/5ore PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ore ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/OCCT_RHIRD OCCT_RHIRD]] Component of the octopine active transport system probably consisting of four subunits: Q, M, P and T.	+	[https://www.uniprot.org/uniprot/OCCT_RHIRD OCCT_RHIRD] Component of the octopine active transport system probably consisting of four subunits: Q, M, P and T.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	~~[[Category: Morera, S]]~~	+	[[Category: Agrobacterium tumefaciens]]
-	~~[[Category: Vigouroux, A]]~~	+	[[Category: Large Structures]]
-	[[Category: Agrobacterium ~~tumefacien~~]]	+	[[Category: Morera S]]
-	[[Category: ~~Arginine~~]]	+	[[Category: Vigouroux A]]
-	[[Category: ~~Bacterial~~]]	+
-	[[Category: ~~Bacterial protein]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Gene expression regulation]]~~	+
-	~~[[Category: Gene]]~~	+
-	~~[[Category: Ligand]]~~	+
-	~~[[Category: Plant tumor]]~~	+
-	~~[[Category: Plasmid~~]]	+

OCA at 05:57, 3 January 2018

2018-01-03T05:57:40Z

←Older revision		Revision as of 05:57, 3 January 2018
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	<StructureSection load='5ore' size='340' side='right' caption='[[5ore]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='5ore' size='340' side='right' caption='[[5ore]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ore]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ORE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ORE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ore]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ORE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ORE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">occT, occJ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 "Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934])</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=5ore FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ore OCA], [http://pdbe.org/5ore PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ore RCSB], [http://www.ebi.ac.uk/pdbsum/5ore PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ore 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=5ore FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ore OCA], [http://pdbe.org/5ore PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ore RCSB], [http://www.ebi.ac.uk/pdbsum/5ore PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ore ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/OCCT_RHIRD OCCT_RHIRD]] Component of the octopine active transport system probably consisting of four subunits: Q, M, P and T.		[[http://www.uniprot.org/uniprot/OCCT_RHIRD OCCT_RHIRD]] Component of the octopine active transport system probably consisting of four subunits: Q, M, P and T.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Agrobacterium pathogens of octopine- and nopaline-types force host plants to produce either octopine or nopaline compounds, which they use as nutrients. Two Agrobacterium ABC-transporters and their cognate periplasmic binding proteins (PBPs) OccJ and NocT import octopine and nopaline/octopine, respectively. Here, we show that both octopine transport and degradation confer a selective advantage to octopine-type A. tumefaciens when it colonizes plants. We report the X-ray structures of the unliganded PBP OccJ and its complex with octopine as well as a structural comparison with NocT and the related PBP LAO from Salmonella enterica, which binds amino acids (lysine, arginine and ornithine). We investigated the specificity of OccJ, NocT and LAO using several ligands such as amino acids, octopine, nopaline and octopine analogues. OccJ displays a high selectivity and nanomolar range affinity for octopine. Altogether, the structural and affinity data allowed to define an octopine binding signature in PBPs and to construct a OccJ mutant impaired in octopine binding, a selective octopine-binding NocT and a non-selective octopine-binding LAO by changing one single residue in these PBPs. We proposed the PBP OccJ as a major trait in the ecological specialization of octopine-type Agrobacterium pathogens when they colonize and exploit the plant host.
		+
		+	Structural basis for high specificity of octopine binding in the plant pathogen Agrobacterium tumefaciens.,Vigouroux A, El Sahili A, Lang J, Aumont-Nicaise M, Dessaux Y, Faure D, Morera S Sci Rep. 2017 Dec 21;7(1):18033. doi: 10.1038/s41598-017-18243-8. PMID:29269740<ref>PMID:29269740</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ore" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:13, 20 December 2017

2017-12-20T06:13:08Z

←Older revision		Revision as of 06:13, 20 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ore ~~is ON HOLD until Paper Publication~~	+	==Structure of the periplasmic binding protein (PBP) OccJ from agrobacterium tumefaciens B6==
-		+	<StructureSection load='5ore' size='340' side='right' caption='[[5ore]], [[Resolution\|resolution]] 2.35Å' scene=''>
-	~~Authors~~: ~~Vigouroux, A~~.~~, El Sahili, A~~.~~, Lang, J~~.~~, Aumont~~-~~Nicaise, M~~.~~, Dessaux, Y~~.~~, Faure, D~~.~~, Morera, S~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ore]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ORE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ORE FirstGlance]. <br>
-	~~Description: Structure of the PBP OccJ~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></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=5ore FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ore OCA], [http://pdbe.org/5ore PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ore RCSB], [http://www.ebi.ac.uk/pdbsum/5ore PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ore ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Faure~~, D]]	+	</table>
-	[[~~Category~~: ~~Aumont~~-~~Nicaise, M~~]]	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/OCCT_RHIRD OCCT_RHIRD]] Component of the octopine active transport system probably consisting of four subunits: Q, M, P and T.
		+	__TOC__
		+	</StructureSection>
	[[Category: Morera, S]]		[[Category: Morera, S]]
-	[[Category: El Sahili, A]]
	[[Category: Vigouroux, A]]		[[Category: Vigouroux, A]]
-	[[Category: ~~Dessaux, Y~~]]	+	[[Category: Agrobacterium tumefacien]]
-	[[Category: ~~Lang, J~~]]	+	[[Category: Arginine]]
		+	[[Category: Bacterial]]
		+	[[Category: Bacterial protein]]
		+	[[Category: Dna]]
		+	[[Category: Gene expression regulation]]
		+	[[Category: Gene]]
		+	[[Category: Ligand]]
		+	[[Category: Plant tumor]]
		+	[[Category: Plasmid]]

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

2017-09-27T12:45:23Z

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

←Older revision

Revision as of 12:45, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5ore is ON HOLD until Paper Publication Authors: Vigouroux, A., El Sahili, A., Lang, J., Aumont-Nicaise, M., Dessaux, Y., Faure, D., Morera, S. Des...

2017-09-27T12:45:22Z

New page: '''Unreleased structure''' The entry 5ore is ON HOLD until Paper Publication Authors: Vigouroux, A., El Sahili, A., Lang, J., Aumont-Nicaise, M., Dessaux, Y., Faure, D., Morera, S. Des...

New page

'''Unreleased structure'''

The entry 5ore is ON HOLD until Paper Publication

Authors: Vigouroux, A., El Sahili, A., Lang, J., Aumont-Nicaise, M., Dessaux, Y., Faure, D., Morera, S.

Description: Structure of the PBP OccJ
[[Category: Unreleased Structures]]
[[Category: Faure, D]]
[[Category: Aumont-Nicaise, M]]
[[Category: Morera, S]]
[[Category: El Sahili, A]]
[[Category: Vigouroux, A]]
[[Category: Dessaux, Y]]
[[Category: Lang, J]]