8ci6 - Revision history

OCA at 08:21, 7 February 2024

OCA — Wed, 07 Feb 2024 08:21:15 GMT

←Older revision		Revision as of 08:21, 7 February 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/B9JXG4_ALLAM B9JXG4_ALLAM]		[https://www.uniprot.org/uniprot/B9JXG4_ALLAM B9JXG4_ALLAM]
-	<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 8ci6" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:25, 24 January 2024

OCA — Wed, 24 Jan 2024 11:25:14 GMT

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

-	~~The entry~~ 8ci6 is ~~ON HOLD until Paper~~ Publication	+	==PBP AccA from A. vitis S4 in complex with D-glucose-2-phosphate (G2P)==
		+	<StructureSection load='8ci6' size='340' side='right'caption='[[8ci6]], [[Resolution\|resolution]] 1.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8ci6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_vitis_S4 Agrobacterium vitis S4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8CI6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8CI6 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]] 1.199Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALX:2-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE'>ALX</scene>, <scene name='pdbligand=BNX:2-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE'>BNX</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=8ci6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ci6 OCA], [https://pdbe.org/8ci6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ci6 RCSB], [https://www.ebi.ac.uk/pdbsum/8ci6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ci6 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B9JXG4_ALLAM B9JXG4_ALLAM]
		+	<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 8ci6" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Agrobacterium vitis S4]]
		+	[[Category: Large Structures]]
		+	[[Category: Morera S]]
		+	[[Category: Vigouroux A]]

OCA at 07:57, 21 June 2023

OCA — Wed, 21 Jun 2023 07:57:41 GMT

←Older revision		Revision as of 07:57, 21 June 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8ci6 is ON HOLD	+	The entry 8ci6 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 05:20, 3 May 2023

OCA — Wed, 03 May 2023 05:20:35 GMT

←Older revision		Revision as of 05:20, 3 May 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8ci6 is ON HOLD ~~until sometime in the future~~	+	The entry 8ci6 is ON HOLD

	Authors:		Authors:

OCA: Protected "8ci6" [edit=sysop:move=sysop]

OCA — Wed, 15 Feb 2023 08:39:21 GMT

Protected "8ci6" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:39, 15 February 2023

OCA: New page: '''Unreleased structure''' The entry 8ci6 is ON HOLD until sometime in the future Authors: Description: Category: Unreleased Structures

OCA — Wed, 15 Feb 2023 08:39:20 GMT

New page: '''Unreleased structure''' The entry 8ci6 is ON HOLD until sometime in the future Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8ci6 is ON HOLD until sometime in the future

Authors:

Description:
[[Category: Unreleased Structures]]