4p0i - Revision history

OCA at 00:38, 28 December 2023

2023-12-28T00:38:47Z

←Older revision		Revision as of 00:38, 28 December 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4p0i]] 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=4P0I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4P0I FirstGlance]. <br>		<table><tr><td colspan='2'>[[4p0i]] 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=4P0I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4P0I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.89Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=4p0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p0i OCA], [https://pdbe.org/4p0i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4p0i RCSB], [https://www.ebi.ac.uk/pdbsum/4p0i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4p0i 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=4p0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p0i OCA], [https://pdbe.org/4p0i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4p0i RCSB], [https://www.ebi.ac.uk/pdbsum/4p0i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4p0i ProSAT]</span></td></tr>
	</table>		</table>

OCA at 12:35, 1 February 2023

2023-02-01T12:35:25Z

←Older revision		Revision as of 12:35, 1 February 2023
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	<StructureSection load='4p0i' size='340' side='right'caption='[[4p0i]], [[Resolution\|resolution]] 1.89Å' scene=''>		<StructureSection load='4p0i' size='340' side='right'caption='[[4p0i]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4p0i]] 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=4P0I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4P0I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4p0i]] 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=4P0I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4P0I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pow\|4pow]], [[4pox\|4pox]], [[4pp0\|4pp0]]</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=4p0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p0i OCA], [https://pdbe.org/4p0i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4p0i RCSB], [https://www.ebi.ac.uk/pdbsum/4p0i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4p0i 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~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4p0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p0i OCA], [~~http~~://pdbe.org/4p0i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4p0i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4p0i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4p0i ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[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 22:		Line 22:
	__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: Periplasmic binding protein]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 08:19, 17 April 2019

2019-04-17T08:19:49Z

←Older revision		Revision as of 08:19, 17 April 2019
Line 1:		Line 1:

	==Structure of the PBP NocT==		==Structure of the PBP NocT==
-	<StructureSection load='4p0i' size='340' side='right' caption='[[4p0i]], [[Resolution\|resolution]] 1.89Å' scene=''>	+	<StructureSection load='4p0i' size='340' side='right'caption='[[4p0i]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4p0i]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P0I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4P0I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4p0i]] 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=4P0I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4P0I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pow\|4pow]], [[4pox\|4pox]], [[4pp0\|4pp0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pow\|4pow]], [[4pox\|4pox]], [[4pp0\|4pp0]]</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=4p0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p0i OCA], [http://pdbe.org/4p0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4p0i RCSB], [http://www.ebi.ac.uk/pdbsum/4p0i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4p0i 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=4p0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p0i OCA], [http://pdbe.org/4p0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4p0i RCSB], [http://www.ebi.ac.uk/pdbsum/4p0i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4p0i ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Agrfc]]
		+	[[Category: Large Structures]]
	[[Category: Morera, S]]		[[Category: Morera, S]]
	[[Category: Vigouroux, A]]		[[Category: Vigouroux, A]]
	[[Category: Periplasmic binding protein]]		[[Category: Periplasmic binding protein]]
	[[Category: Transport protein]]		[[Category: Transport protein]]

OCA at 11:27, 11 August 2016

2016-08-11T11:27:12Z

←Older revision		Revision as of 11:27, 11 August 2016
Line 1:		Line 1:
		+
	==Structure of the PBP NocT==		==Structure of the PBP NocT==
	<StructureSection load='4p0i' size='340' side='right' caption='[[4p0i]], [[Resolution\|resolution]] 1.89Å' scene=''>		<StructureSection load='4p0i' size='340' side='right' caption='[[4p0i]], [[Resolution\|resolution]] 1.89Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pow\|4pow]], [[4pox\|4pox]], [[4pp0\|4pp0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pow\|4pow]], [[4pox\|4pox]], [[4pp0\|4pp0]]</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=4p0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p0i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4p0i RCSB], [http://www.ebi.ac.uk/pdbsum/4p0i PDBsum]</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=4p0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p0i OCA], [http://pdbe.org/4p0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4p0i RCSB], [http://www.ebi.ac.uk/pdbsum/4p0i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4p0i ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4p0i" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:29, 25 January 2015

2015-01-25T09:29:34Z

←Older revision		Revision as of 09:29, 25 January 2015
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Morera, S.]]	+	[[Category: Morera, S]]
-	[[Category: Vigouroux, A.]]	+	[[Category: Vigouroux, A]]
	[[Category: Periplasmic binding protein]]		[[Category: Periplasmic binding protein]]
	[[Category: Transport protein]]		[[Category: Transport protein]]

OCA at 09:31, 29 October 2014

2014-10-29T09:31:25Z

←Older revision		Revision as of 09:31, 29 October 2014
Line 1:		Line 1:
-	==~~Structural~~ of ~~periplasmic binding protein~~==	+	==Structure of the PBP NocT==
	<StructureSection load='4p0i' size='340' side='right' caption='[[4p0i]], [[Resolution\|resolution]] 1.89Å' scene=''>		<StructureSection load='4p0i' size='340' side='right' caption='[[4p0i]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==

OCA at 11:41, 22 October 2014

2014-10-22T11:41:07Z

←Older revision		Revision as of 11:41, 22 October 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structural of periplasmic binding protein==
		+	<StructureSection load='4p0i' size='340' side='right' caption='[[4p0i]], [[Resolution\|resolution]] 1.89Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4p0i]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P0I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4P0I FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pow\|4pow]], [[4pox\|4pox]], [[4pp0\|4pp0]]</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=4p0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p0i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4p0i RCSB], [http://www.ebi.ac.uk/pdbsum/4p0i PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	By modifying the nuclear genome of its host, the plant pathogen Agrobacterium tumefaciens induces the development of plant tumours in which it proliferates. The transformed plant tissues accumulate uncommon low molecular weight compounds called opines that are growth substrates for A. tumefaciens. In the pathogen-induced niche (the plant tumour), a selective advantage conferred by opine assimilation has been hypothesized, but not experimentally demonstrated. Here, using genetics and structural biology, we deciphered how the pathogen is able to bind opines and use them to efficiently compete in the plant tumour. We report high resolution X-ray structures of the periplasmic binding protein (PBP) NocT unliganded and liganded with the opine nopaline (a condensation product of arginine and alpha-ketoglurate) and its lactam derivative pyronopaline. NocT exhibited an affinity for pyronopaline (KD of 0.6 microM) greater than that for nopaline (KD of 3.7 microM). Although the binding-mode of the arginine part of nopaline/pyronopaline in NocT resembled that of arginine in other PBPs, affinity measurement by two different techniques showed that NocT did not bind arginine. In contrast, NocT presented specific residues such as M117 to stabilize the bound opines. NocT relatives that exhibit the nopaline/pyronopaline-binding mode were only found in genomes of the genus Agrobacterium. Transcriptomics and reverse genetics revealed that A. tumefaciens uses the same pathway for assimilating nopaline and pyronopaline. Fitness measurements showed that NocT is required for a competitive colonization of the plant tumour by A. tumefaciens. Moreover, even though the Ti-plasmid conjugal transfer was not regulated by nopaline, the competitive advantage gained by the nopaline-assimilating Ti-plasmid donors led to a preferential horizontal propagation of this Ti-plasmid amongst the agrobacteria colonizing the plant-tumour niche. This work provided structural and genetic evidences to support the niche construction paradigm in bacterial pathogens.

-	~~The entry 4p0i is ON HOLD until Paper Publication~~	+	Agrobacterium uses a unique ligand-binding mode for trapping opines and acquiring a competitive advantage in the niche construction on plant host.,Lang J, Vigouroux A, Planamente S, El Sahili A, Blin P, Aumont-Nicaise M, Dessaux Y, Morera S, Faure D PLoS Pathog. 2014 Oct 9;10(10):e1004444. doi: 10.1371/journal.ppat.1004444., eCollection 2014 Oct. PMID:25299655<ref>PMID:25299655</ref>

-	~~Authors: Vigouroux~~, A., Morera, S.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Structural of periplasmic~~ binding protein	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Morera, S.]]
		+	[[Category: Vigouroux, A.]]
		+	[[Category: Periplasmic binding protein]]
		+	[[Category: Transport protein]]

OCA at 07:20, 23 April 2014

2014-04-23T07:20:58Z

←Older revision		Revision as of 07:20, 23 April 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4p0i is ON HOLD	+	The entry 4p0i is ON HOLD until Paper Publication

	Authors: Vigouroux, A., Morera, S.		Authors: Vigouroux, A., Morera, S.

	Description: Structural of periplasmic binding protein		Description: Structural of periplasmic binding protein

OCA: Protected "4p0i" [edit=sysop:move=sysop]

2014-03-12T12:26:36Z

Protected "4p0i" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:26, 12 March 2014

OCA: New page: '''Unreleased structure''' The entry 4p0i is ON HOLD Authors: Vigouroux, A., Morera, S. Description: Structural of periplasmic binding protein

2014-03-12T12:26:35Z

New page: '''Unreleased structure''' The entry 4p0i is ON HOLD Authors: Vigouroux, A., Morera, S. Description: Structural of periplasmic binding protein

New page

'''Unreleased structure'''

The entry 4p0i is ON HOLD

Authors: Vigouroux, A., Morera, S.

Description: Structural of periplasmic binding protein