8cke - Revision history

OCA at 08:21, 7 February 2024

OCA — Wed, 07 Feb 2024 08:21:25 GMT

←Older revision		Revision as of 08:21, 7 February 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q52012_AGRFC Q52012_AGRFC]		[https://www.uniprot.org/uniprot/Q52012_AGRFC Q52012_AGRFC]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Plants genetically modified by the pathogenic Agrobacterium strain C58 synthesize agrocinopines A and B, whereas those modified by the pathogenic strain Bo542 produce agrocinopines C and D. The four agrocinopines (A, B, C and D) serve as nutrients by agrobacteria and signaling molecule for the dissemination of virulence genes. They share the uncommon pyranose-2-phosphate motif, represented by the L-arabinopyranose moiety in agrocinopines A/B and the D-glucopyranose moiety in agrocinopines C/D, also found in the antibiotic agrocin 84. They are imported into agrobacterial cytoplasm via the Acc transport system, including the solute-binding protein AccA coupled to an ABC transporter. We have previously shown that unexpectedly, AccA from strain C58 (AccAC58) recognizes the pyranose-2-phosphate motif present in all four agrocinopines and agrocin 84, meaning that strain C58 is able to import agrocinopines C/D, originating from the competitor strain Bo542. Here, using agrocinopine derivatives and combining crystallography, affinity and stability measurements, modeling, molecular dynamics, in vitro and vivo assays, we show that AccABo542 and AccAC58 behave differently despite 75% sequence identity and a nearly identical ligand binding site. Indeed, strain Bo542 imports only compounds containing the D-glucopyranose-2-phosphate moiety, and with a lower affinity compared to strain C58. This difference in import efficiency makes C58 more competitive than Bo542 in culture media. We can now explain why Agrobacterium/Allorhizobium vitis strain S4 is insensitive to agrocin 84, although its genome contains a conserved Acc transport system. Overall, our work highlights AccA proteins as a case study, for which stability and dynamics drive specificity.
-
-	A highly conserved ligand-binding site for AccA transporters of antibiotic and quorum-sensing regulator in Agrobacterium leads to a different specificity.,Morera S, Vigouroux A, Aumont-Nicaise M, Ahmar M, Meyer T, El Sahili A, Deicsics G, Gonzalez-Mula A, Li S, Dore J, Siragu S, Legrand P, Penot C, Andre F, Faure D, Soulere L, Queneau Y, Vial L Biochem J. 2023 Dec 6:BCJ20230273. doi: 10.1042/BCJ20230273. PMID:38058289<ref>PMID:38058289</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 8cke" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:25, 24 January 2024

OCA — Wed, 24 Jan 2024 11:25:16 GMT

←Older revision		Revision as of 11:25, 24 January 2024
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8cke is ~~ON HOLD until Paper~~ Publication	+	==PBP AccA from A.tumefaciens C58 in complex with agrocinopine A in space group I222==
		+	<StructureSection load='8cke' size='340' side='right'caption='[[8cke]], [[Resolution\|resolution]] 1.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8cke]] is a 1 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=8CKE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8CKE FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.298Å</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=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=LAO:2-O-PHOSPHONO-ALPHA-L-ARABINOPYRANOSE'>LAO</scene>, <scene name='pdbligand=PRD_002470:Agrocinopine+A+(alpha-L-arabinopyranose+form)'>PRD_002470</scene>, <scene name='pdbligand=PRD_002473:Agrocinopine+A+(beta-L-arabinopyranose+form)'>PRD_002473</scene>, <scene name='pdbligand=VDF:2-O-phosphono-beta-L-arabinopyranose'>VDF</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=8cke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8cke OCA], [https://pdbe.org/8cke PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8cke RCSB], [https://www.ebi.ac.uk/pdbsum/8cke PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8cke ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q52012_AGRFC Q52012_AGRFC]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Plants genetically modified by the pathogenic Agrobacterium strain C58 synthesize agrocinopines A and B, whereas those modified by the pathogenic strain Bo542 produce agrocinopines C and D. The four agrocinopines (A, B, C and D) serve as nutrients by agrobacteria and signaling molecule for the dissemination of virulence genes. They share the uncommon pyranose-2-phosphate motif, represented by the L-arabinopyranose moiety in agrocinopines A/B and the D-glucopyranose moiety in agrocinopines C/D, also found in the antibiotic agrocin 84. They are imported into agrobacterial cytoplasm via the Acc transport system, including the solute-binding protein AccA coupled to an ABC transporter. We have previously shown that unexpectedly, AccA from strain C58 (AccAC58) recognizes the pyranose-2-phosphate motif present in all four agrocinopines and agrocin 84, meaning that strain C58 is able to import agrocinopines C/D, originating from the competitor strain Bo542. Here, using agrocinopine derivatives and combining crystallography, affinity and stability measurements, modeling, molecular dynamics, in vitro and vivo assays, we show that AccABo542 and AccAC58 behave differently despite 75% sequence identity and a nearly identical ligand binding site. Indeed, strain Bo542 imports only compounds containing the D-glucopyranose-2-phosphate moiety, and with a lower affinity compared to strain C58. This difference in import efficiency makes C58 more competitive than Bo542 in culture media. We can now explain why Agrobacterium/Allorhizobium vitis strain S4 is insensitive to agrocin 84, although its genome contains a conserved Acc transport system. Overall, our work highlights AccA proteins as a case study, for which stability and dynamics drive specificity.

-	~~Authors~~:	+	A highly conserved ligand-binding site for AccA transporters of antibiotic and quorum-sensing regulator in Agrobacterium leads to a different specificity.,Morera S, Vigouroux A, Aumont-Nicaise M, Ahmar M, Meyer T, El Sahili A, Deicsics G, Gonzalez-Mula A, Li S, Dore J, Siragu S, Legrand P, Penot C, Andre F, Faure D, Soulere L, Queneau Y, Vial L Biochem J. 2023 Dec 6:BCJ20230273. doi: 10.1042/BCJ20230273. PMID:38058289<ref>PMID:38058289</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8cke" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Agrobacterium fabrum str. C58]]
		+	[[Category: Large Structures]]
		+	[[Category: Morera S]]
		+	[[Category: Vigouroux A]]

OCA at 09:47, 13 December 2023

OCA — Wed, 13 Dec 2023 09:47:53 GMT

←Older revision		Revision as of 09:47, 13 December 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8cke is ON HOLD	+	The entry 8cke is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8cke" [edit=sysop:move=sysop]

OCA — Wed, 22 Feb 2023 09:44:20 GMT

Protected "8cke" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:44, 22 February 2023

OCA: New page: '''Unreleased structure''' The entry 8cke is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 22 Feb 2023 09:44:09 GMT

New page: '''Unreleased structure''' The entry 8cke is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8cke is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]