5ub4 - Revision history

OCA at 14:26, 6 March 2024

2024-03-06T14:26:02Z

←Older revision		Revision as of 14:26, 6 March 2024
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	<StructureSection load='5ub4' size='340' side='right'caption='[[5ub4]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='5ub4' size='340' side='right'caption='[[5ub4]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ub4]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Xanac Xanac~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UB4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UB4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ub4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_citri_pv._citri_str._306 Xanthomonas citri pv. citri str. 306]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UB4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UB4 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CL:CHLORIDE+ION'>CL</scene~~>, ~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.09Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5ub3\|5ub3]], [[5ub6\|5ub6]], [[5ub7\|5ub7]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">XAC2383 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190486 XANAC])~~</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=5ub4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ub4 OCA], [https://pdbe.org/5ub4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ub4 RCSB], [https://www.ebi.ac.uk/pdbsum/5ub4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ub4 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=5ub4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ub4 OCA], [~~http~~://pdbe.org/5ub4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ub4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ub4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ub4 ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q8PJZ4_XANAC Q8PJZ4_XANAC]
-	The second messenger cyclic diguanylate monophosphate (c-di-GMP) is a central regulator of bacterial lifestyle, controlling several behaviors, including the switch between sessile and motile states. The c-di-GMP levels are controlled by the interplay between diguanylate cyclases (DGCs) and phosphodiesterases, which synthesize and hydrolyze this second messenger, respectively. These enzymes often contain additional domains that regulate activity via binding of small molecules, covalent modification, or protein-protein interactions. A major challenge remains to understand how DGC activity is regulated by these additional domains or interaction partners in specific signaling pathways. Here, we identified a pair of co-transcribed genes (xac2382 and xac2383) in the phytopathogenic, Gram-negative bacterium Xanthomonas citri subsp. citri (Xac), whose mutations resulted in opposing motility phenotypes. We show that the periplasmic cache domain of XAC2382, a membrane-associated DGC, interacts with XAC2383, a periplasmic binding protein, and we provide evidence that this interaction regulates XAC2382 DGC activity. Moreover, we solved the crystal structure of XAC2383 with different ligands, indicating a preference for negatively charged phosphate-containing compounds. We propose that XAC2383 acts as a periplasmic sensor that, upon binding its ligand, inhibits the DGC activity of XAC2382. Of note, we also found that this previously uncharacterized signal transduction system is present in several other bacterial phyla, including Gram-positive bacteria. Phylogenetic analysis of homologs of the XAC2382-XAC2383 pair supports several independent origins that created new combinations of XAC2382 homologs with a conserved periplasmic cache domain with different cytoplasmic output module architectures.	+
-		+
-	A bipartite periplasmic receptor-diguanylate cyclase pair (XAC2383-XAC2382) in the bacterium Xanthomonas citri.,Teixeira RD, Guzzo CR, Arevalo SJ, Andrade MO, Abrahao J, de Souza RF, Farah CS J Biol Chem. 2018 Jul 6;293(27):~~10767-10781. doi: 10.1074~~/~~jbc.RA118.003475. Epub , 2018 May 4. PMID:29728456<ref>PMID:29728456<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5ub4" style="background-color:#fffaf0;"><~~/~~div>~~	+

	==See Also==		==See Also==
	*[[Phosphate-binding protein\|Phosphate-binding protein]]		*[[Phosphate-binding protein\|Phosphate-binding protein]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Xanac~~]]	+	[[Category: Xanthomonas citri pv. citri str. 306]]
-	[[Category: Farah~~, C S~~]]	+	[[Category: Farah CS]]
-	[[Category: Guzzo~~, C R~~]]	+	[[Category: Guzzo CR]]
-	[[Category: Teixeira~~, R D]]~~	+	[[Category: Teixeira RD]]
-	~~[[Category: Metal binding protein]]~~	+
-	~~[[Category: Periplasmic binding protein periplasmic sensor phosphate ion phosphonate-bd~~]]	+

OCA at 09:14, 1 January 2020

2020-01-01T09:14:20Z

←Older revision		Revision as of 09:14, 1 January 2020
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5ub4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ub4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphate-binding protein\|Phosphate-binding protein]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:27, 17 April 2019

2019-04-17T06:27:37Z

←Older revision		Revision as of 06:27, 17 April 2019
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	==XAC2383 from Xanthomonas citri bound to phosphate==		==XAC2383 from Xanthomonas citri bound to phosphate==
-	<StructureSection load='5ub4' size='340' side='right' caption='[[5ub4]], [[Resolution\|resolution]] 2.09Å' scene=''>	+	<StructureSection load='5ub4' size='340' side='right'caption='[[5ub4]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ub4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UB4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UB4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ub4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Xanac Xanac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UB4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UB4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ub3\|5ub3]], [[5ub6\|5ub6]], [[5ub7\|5ub7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ub3\|5ub3]], [[5ub6\|5ub6]], [[5ub7\|5ub7]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">XAC2383 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190486 XANAC])</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=5ub4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ub4 OCA], [http://pdbe.org/5ub4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ub4 RCSB], [http://www.ebi.ac.uk/pdbsum/5ub4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ub4 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=5ub4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ub4 OCA], [http://pdbe.org/5ub4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ub4 RCSB], [http://www.ebi.ac.uk/pdbsum/5ub4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ub4 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The second messenger cyclic diguanylate monophosphate (c-di-GMP) is a central regulator of bacterial lifestyle, controlling several behaviors, including the switch between sessile and motile states. The c-di-GMP levels are controlled by the interplay between diguanylate cyclases (DGCs) and phosphodiesterases, which synthesize and hydrolyze this second messenger, respectively. These enzymes often contain additional domains that regulate activity via binding of small molecules, covalent modification, or protein-protein interactions. A major challenge remains to understand how DGC activity is regulated by these additional domains or interaction partners in specific signaling pathways. Here, we identified a pair of co-transcribed genes (xac2382 and xac2383) in the phytopathogenic, Gram-negative bacterium Xanthomonas citri subsp. citri (Xac), whose mutations resulted in opposing motility phenotypes. We show that the periplasmic cache domain of XAC2382, a membrane-associated DGC, interacts with XAC2383, a periplasmic binding protein, and we provide evidence that this interaction regulates XAC2382 DGC activity. Moreover, we solved the crystal structure of XAC2383 with different ligands, indicating a preference for negatively charged phosphate-containing compounds. We propose that XAC2383 acts as a periplasmic sensor that, upon binding its ligand, inhibits the DGC activity of XAC2382. Of note, we also found that this previously uncharacterized signal transduction system is present in several other bacterial phyla, including Gram-positive bacteria. Phylogenetic analysis of homologs of the XAC2382-XAC2383 pair supports several independent origins that created new combinations of XAC2382 homologs with a conserved periplasmic cache domain with different cytoplasmic output module architectures.
		+
		+	A bipartite periplasmic receptor-diguanylate cyclase pair (XAC2383-XAC2382) in the bacterium Xanthomonas citri.,Teixeira RD, Guzzo CR, Arevalo SJ, Andrade MO, Abrahao J, de Souza RF, Farah CS J Biol Chem. 2018 Jul 6;293(27):10767-10781. doi: 10.1074/jbc.RA118.003475. Epub , 2018 May 4. PMID:29728456<ref>PMID:29728456</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ub4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Xanac]]
	[[Category: Farah, C S]]		[[Category: Farah, C S]]
	[[Category: Guzzo, C R]]		[[Category: Guzzo, C R]]

OCA at 08:26, 10 January 2018

2018-01-10T08:26:09Z

←Older revision		Revision as of 08:26, 10 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ub4 is ~~ON HOLD until Paper Publication~~	+	==XAC2383 from Xanthomonas citri bound to phosphate==
-		+	<StructureSection load='5ub4' size='340' side='right' caption='[[5ub4]], [[Resolution\|resolution]] 2.09Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ub4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UB4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UB4 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ub3\|5ub3]], [[5ub6\|5ub6]], [[5ub7\|5ub7]]</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=5ub4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ub4 OCA], [http://pdbe.org/5ub4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ub4 RCSB], [http://www.ebi.ac.uk/pdbsum/5ub4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ub4 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Farah, C S]]
		+	[[Category: Guzzo, C R]]
		+	[[Category: Teixeira, R D]]
		+	[[Category: Metal binding protein]]
		+	[[Category: Periplasmic binding protein periplasmic sensor phosphate ion phosphonate-bd]]

OCA at 10:59, 5 April 2017

2017-04-05T10:59:22Z

←Older revision		Revision as of 10:59, 5 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ub4 is ON HOLD	+	The entry 5ub4 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5ub4" [edit=sysop:move=sysop]

2017-01-02T15:18:45Z

Protected "5ub4" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:18, 2 January 2017

OCA: New page: '''Unreleased structure''' The entry 5ub4 is ON HOLD Authors: Description: Category: Unreleased Structures

2017-01-02T15:18:44Z

New page: '''Unreleased structure''' The entry 5ub4 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5ub4 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]