5otc - Revision history

OCA at 01:23, 28 December 2023

OCA — Thu, 28 Dec 2023 01:23:46 GMT

←Older revision		Revision as of 01:23, 28 December 2023
Line 1:		Line 1:

	==Structure of the periplasmic binding protein (PBP) NocT from Agrobacterium tumefaciens C58 in complex with noroctopinic acid.==		==Structure of the periplasmic binding protein (PBP) NocT from Agrobacterium tumefaciens C58 in complex with noroctopinic acid.==
-	<StructureSection load='5otc' size='340' side='right' caption='[[5otc]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5otc' size='340' side='right'caption='[[5otc]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5otc]] 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=5OTC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OTC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5otc]] 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=5OTC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OTC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AQK:(2~{S})-5-azanyl-2-(2-hydroxy-2-oxoethylamino)pentanoic+acid'>AQK</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 2.2Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AQK:(2~{S})-5-azanyl-2-(2-hydroxy-2-oxoethylamino)pentanoic+acid'>AQK</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=5otc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5otc OCA], [~~http~~://pdbe.org/5otc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5otc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5otc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5otc 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=5otc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5otc OCA], [https://pdbe.org/5otc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5otc RCSB], [https://www.ebi.ac.uk/pdbsum/5otc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5otc 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 ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	~~[[Category: Agrfc]]~~	+	[[Category: Agrobacterium fabrum str. C58]]
-	~~[[Category: Morera, S]]~~	+	[[Category: Large Structures]]
-	~~[[Category: Vigouroux, A]]~~	+	[[Category: Morera S]]
-	[[Category: Agrobacterium ~~tumefacien~~]]	+	[[Category: Vigouroux A]]
-	[[Category: ~~Arginine~~]]	+
-	[[Category: ~~Bacterial~~]]	+
-	[[Category: ~~Bacterial protein]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Gene expression regulation]]~~	+
-	~~[[Category: Gene]]~~	+
-	~~[[Category: Ligand]]~~	+
-	~~[[Category: Plant tumor]]~~	+
-	~~[[Category: Plasmid]]~~	+
-	~~[[Category: Protein binding~~]]	+

OCA at 05:58, 3 January 2018

OCA — Wed, 03 Jan 2018 05:58:18 GMT

←Older revision		Revision as of 05:58, 3 January 2018
Line 3:		Line 3:
	<StructureSection load='5otc' size='340' side='right' caption='[[5otc]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5otc' size='340' side='right' caption='[[5otc]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5otc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OTC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OTC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5otc]] 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=5OTC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OTC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AQK:(2~{S})-5-azanyl-2-(2-hydroxy-2-oxoethylamino)pentanoic+acid'>AQK</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AQK:(2~{S})-5-azanyl-2-(2-hydroxy-2-oxoethylamino)pentanoic+acid'>AQK</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5otc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5otc OCA], [http://pdbe.org/5otc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5otc RCSB], [http://www.ebi.ac.uk/pdbsum/5otc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5otc 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=5otc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5otc OCA], [http://pdbe.org/5otc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5otc RCSB], [http://www.ebi.ac.uk/pdbsum/5otc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5otc 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.		[[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 ==
		+	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 5otc" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Agrfc]]
	[[Category: Morera, S]]		[[Category: Morera, S]]
	[[Category: Vigouroux, A]]		[[Category: Vigouroux, A]]

OCA at 06:13, 20 December 2017

OCA — Wed, 20 Dec 2017 06:13:36 GMT

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

-	~~The entry 5otc is ON HOLD until Paper Publication~~	+	==Structure of the periplasmic binding protein (PBP) NocT from Agrobacterium tumefaciens C58 in complex with noroctopinic acid.==
-		+	<StructureSection load='5otc' size='340' side='right' caption='[[5otc]], [[Resolution\|resolution]] 2.20Å' 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'>[[5otc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OTC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OTC FirstGlance]. <br>
-	~~Description:~~ Structure of the periplasmic binding protein NocT from A.tumefaciens in complex with noroctopinic acid	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AQK:(2~{S})-5-azanyl-2-(2-hydroxy-2-oxoethylamino)pentanoic+acid'>AQK</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=5otc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5otc OCA], [http://pdbe.org/5otc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5otc RCSB], [http://www.ebi.ac.uk/pdbsum/5otc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5otc ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Faure, D~~]]	+	</table>
-	[[~~Category~~: ~~Aumont~~-~~Nicaise~~, M]]	+	== 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.
		+	__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]]
		+	[[Category: Protein binding]]

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

OCA — Wed, 27 Sep 2017 12:49:56 GMT

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

←Older revision

Revision as of 12:49, 27 September 2017

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

OCA — Wed, 27 Sep 2017 12:49:55 GMT

New page: '''Unreleased structure''' The entry 5otc 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 5otc 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 periplasmic binding protein NocT from A.tumefaciens in complex with noroctopinic acid
[[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]]