6hlx - Revision history

OCA at 11:32, 24 January 2024

2024-01-24T11:32:43Z

←Older revision		Revision as of 11:32, 24 January 2024
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	==Structure of the PBP AgaA in complex with agropinic acid from A.tumefacien R10==		==Structure of the PBP AgaA in complex with agropinic acid from A.tumefacien R10==
-	<StructureSection load='6hlx' size='340' side='right' caption='[[6hlx]], [[Resolution\|resolution]] 1.65Å' scene=''>	+	<StructureSection load='6hlx' size='340' side='right'caption='[[6hlx]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6hlx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HLX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6HLX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6hlx]] 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=6HLX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6HLX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=G9Z:agropinic+acid'>G9Z</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.65Å</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=6hlx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hlx OCA], [~~http~~://pdbe.org/6hlx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6hlx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6hlx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6hlx ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=G9Z:agropinic+acid'>G9Z</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6hlx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hlx OCA], [https://pdbe.org/6hlx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6hlx RCSB], [https://www.ebi.ac.uk/pdbsum/6hlx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6hlx ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O50260_RHIRD O50260_RHIRD]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Marty, L~~]]	+	[[Category: Agrobacterium tumefaciens]]
-	[[Category: ~~Morera, S~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Vigouroux, A~~]]	+	[[Category: Marty L]]
-	[[Category: ~~Abc transporter~~]]	+	[[Category: Morera S]]
-	[[Category: ~~Periplasmic binding protein]]~~	+	[[Category: Vigouroux A]]
-	~~[[Category: Transport protein~~]]	+

OCA at 08:22, 26 December 2018

2018-12-26T08:22:23Z

←Older revision		Revision as of 08:22, 26 December 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 6hlx is ~~ON HOLD until Paper~~ Publication	+	==Structure of the PBP AgaA in complex with agropinic acid from A.tumefacien R10==
		+	<StructureSection load='6hlx' size='340' side='right' caption='[[6hlx]], [[Resolution\|resolution]] 1.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6hlx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HLX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HLX FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=G9Z:agropinic+acid'>G9Z</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6hlx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hlx OCA], [http://pdbe.org/6hlx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hlx RCSB], [http://www.ebi.ac.uk/pdbsum/6hlx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hlx ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Agrobacterium tumefaciens pathogens genetically modify their host plants to drive the synthesis of opines in plant tumors. The mannityl-opine family encompasses mannopine, mannopinic acid, agropine and agropinic acid. These opines serve as nutrients and are imported into bacteria via periplasmic binding proteins (PBPs) in association with ABC transporters. Structural and affinity data on agropine and agropinic acid opines bound to PBPs are currently lacking. Here, we investigated the molecular basis of AgtB and AgaA, proposed as the specific PBP for agropine and agropinic acid import, respectively. Using genetic approaches and affinity measurements, we identified AgtB and its transporter as responsible for agropine uptake in agropine-assimilating agrobacteria. Nonetheless, we showed that AgtB binds agropinic acid with a higher affinity than agropine, and we structurally characterized the agropinic acid binding mode through three crystal structures at 1.4, 1.74 and 1.9 A resolution. In the crystallization time course, obtaining a crystal structure of AgtB with agropine was unsuccessful due to the spontaneous lactamization of agropine into agropinic acid. AgaA binds agropinic acid only with a similar affinity in nanomolar range as AgtB. The structure of AgaA bound to agropinic acid at 1.65 A resolution defines a different agropinic acid binding signature. Our work highlights the structural and functional characteristics of two efficient agropinic acid assimilation pathways, of which one is also involved in agropine assimilation.

-	~~Authors: Morera, S~~., Marty, L., Vigouroux, A.	+	Structural basis for two efficient modes of agropinic acid opine import into the bacterial pathogen Agrobacterium tumefaciens.,Marty L, Vigouroux A, Aumont-Nicaise M, Pelissier F, Meyer T, Lavire CL, Dessaux Y, Morera S Biochem J. 2018 Dec 14. pii: BCJ20180861. doi: 10.1042/BCJ20180861. PMID:30552142<ref>PMID:30552142</ref>

-	~~Description: Structure~~ of the ~~PBP AgaA in complex with agropinic acid from A~~.~~tumefacien R10~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6hlx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Marty, L]]
	[[Category: Morera, S]]		[[Category: Morera, S]]
	[[Category: Vigouroux, A]]		[[Category: Vigouroux, A]]
-	[[Category: ~~Marty, L~~]]	+	[[Category: Abc transporter]]
		+	[[Category: Periplasmic binding protein]]
		+	[[Category: Transport protein]]

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

2018-09-19T18:12:21Z

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

←Older revision

Revision as of 18:12, 19 September 2018

OCA: New page: '''Unreleased structure''' The entry 6hlx is ON HOLD until Paper Publication Authors: Morera, S., Marty, L., Vigouroux, A. Description: Structure of the PBP AgaA in complex with agropi...

2018-09-19T18:12:19Z

New page: '''Unreleased structure''' The entry 6hlx is ON HOLD until Paper Publication Authors: Morera, S., Marty, L., Vigouroux, A. Description: Structure of the PBP AgaA in complex with agropi...

New page

'''Unreleased structure'''

The entry 6hlx is ON HOLD until Paper Publication

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

Description: Structure of the PBP AgaA in complex with agropinic acid from A.tumefacien R10
[[Category: Unreleased Structures]]
[[Category: Morera, S]]
[[Category: Vigouroux, A]]
[[Category: Marty, L]]