OCA at 11:00, 24 December 2020

OCA — Thu, 24 Dec 2020 11:00:12 GMT

←Older revision		Revision as of 11:00, 24 December 2020
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	==Structure of the transcriptional repressor Atu1419 (VanR) in complex with a fortuitous citrate from agrobacterium fabrum==		==Structure of the transcriptional repressor Atu1419 (VanR) in complex with a fortuitous citrate from agrobacterium fabrum==
-	<StructureSection load='6z74' size='340' side='right'caption='[[6z74]]' scene=''>	+	<StructureSection load='6z74' size='340' side='right'caption='[[6z74]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Z74 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Z74 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6z74]] is a 4 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=6Z74 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Z74 FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6z74 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z74 OCA], [http://pdbe.org/6z74 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6z74 RCSB], [http://www.ebi.ac.uk/pdbsum/6z74 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6z74 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Atu1419 ([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://proteopedia.org/fgij/fg.htm?mol=6z74 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z74 OCA], [http://pdbe.org/6z74 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6z74 RCSB], [http://www.ebi.ac.uk/pdbsum/6z74 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6z74 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A species-specific region, denoted SpG8-1b allowing hydroxycinnamic acids (HCAs) degradation is important for the transition between the two lifestyles (rhizospheric versus pathogenic) of the plant pathogen Agrobacterium fabrum. Indeed, HCAs can be either used as trophic resources and/or as induced-virulence molecules. The SpG8-1b region is regulated by two transcriptional regulators, namely, HcaR (Atu1422) and Atu1419. In contrast to HcaR, Atu1419 remains so far uncharacterized. The high-resolution crystal structures of two fortuitous citrate complexes, two DNA complexes and the apoform revealed that the tetrameric Atu1419 transcriptional regulator belongs to the VanR group of Pfam PF07729 subfamily of the large GntR superfamily. Until now, GntR regulators were described as dimers. Here, we showed that Atu1419 represses three genes of the HCAs catabolic pathway. We characterized both the effector and DNA binding sites and identified key nucleotides in the target palindrome. From promoter activity measurement using defective gene mutants, structural analysis and gel-shift assays, we propose N5,N10-methylenetetrahydrofolate as the effector molecule, which is not a direct product/substrate of the HCA degradation pathway. The Zn2+ ion present in the effector domain has both a structural and regulatory role. Overall, our work shed light on the allosteric mechanism of transcription employed by this GntR repressor.
		+
		+	Characterization of the first tetrameric transcription factor of the GntR superfamily with allosteric regulation from the bacterial pathogen Agrobacterium fabrum.,Vigouroux A, Meyer T, Naretto A, Legrand P, Aumont-Nicaise M, Di Cicco A, Renoud S, Dore J, Levy D, Vial L, Lavire C, Morera S Nucleic Acids Res. 2020 Dec 11. pii: 6031445. doi: 10.1093/nar/gkaa1181. PMID:33313837<ref>PMID:33313837</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6z74" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Agrfc]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Morera S]]	+	[[Category: Morera, S]]
-	[[Category: Vigouroux V]]	+	[[Category: Vigouroux, V]]
		+	[[Category: Transcription]]
		+	[[Category: Transcriptional repressor]]

OCA at 07:48, 2 December 2020

OCA — Wed, 02 Dec 2020 07:48:26 GMT

←Older revision		Revision as of 07:48, 2 December 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6z74 ~~is ON HOLD until Paper Publication~~	+	==Structure of the transcriptional repressor Atu1419 (VanR) in complex with a fortuitous citrate from agrobacterium fabrum==
-		+	<StructureSection load='6z74' size='340' side='right'caption='[[6z74]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Z74 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Z74 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6z74 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z74 OCA], [http://pdbe.org/6z74 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6z74 RCSB], [http://www.ebi.ac.uk/pdbsum/6z74 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6z74 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Morera S]]
		+	[[Category: Vigouroux V]]

OCA: Protected "6z74" [edit=sysop:move=sysop]

OCA — Wed, 10 Jun 2020 05:07:21 GMT

Protected "6z74" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:07, 10 June 2020

OCA: New page: '''Unreleased structure''' The entry 6z74 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 10 Jun 2020 05:07:20 GMT

New page: '''Unreleased structure''' The entry 6z74 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6z74 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]

6z74 - Revision history

OCA at 11:00, 24 December 2020

OCA at 07:48, 2 December 2020

OCA: Protected "6z74" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 6z74 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures