6gcv - Revision history

OCA at 12:35, 9 May 2024

OCA — Thu, 09 May 2024 12:35:05 GMT

←Older revision		Revision as of 12:35, 9 May 2024
Line 1:		Line 1:

	==Ligand binding domain (LBD) of the p. aeruginosa nitrate receptor McpN==		==Ligand binding domain (LBD) of the p. aeruginosa nitrate receptor McpN==
-	<StructureSection load='6gcv' size='340' side='right' caption='[[6gcv]], [[Resolution\|resolution]] 1.30Å' scene=''>	+	<StructureSection load='6gcv' size='340' side='right'caption='[[6gcv]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6gcv]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GCV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6GCV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6gcv]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GCV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6GCV 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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</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]] 1.3Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pctC_5, pctC_1, AOY09_04118, CAZ03_12680, CAZ10_05855, PAMH19_2341, RW109_RW109_03190 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</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=6gcv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gcv OCA], [~~http~~://pdbe.org/6gcv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6gcv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6gcv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6gcv ProSAT]</span></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=6gcv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gcv OCA], [https://pdbe.org/6gcv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6gcv RCSB], [https://www.ebi.ac.uk/pdbsum/6gcv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6gcv ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/MCPN_PSEAE MCPN_PSEAE] Chemotactic-signal transducers respond to changes in the concentration of attractants and repellents in the environment, transduce a signal from the outside to the inside of the cell, and facilitate sensory adaptation through the variation of the level of methylation. McpN is a chemoreceptor that recognizes specifically nitrate and mediates chemoattraction. Binds nitrate specifically and shows no affinity for other ligands such as nitrite. McpN-mediated taxis occurs only under nitrate starvation conditions.<ref>PMID:30782655</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Gavira, J A]]~~	+	[[Category: Large Structures]]
-	~~[[Category: Krell, T]]~~	+
-	~~[[Category: Martin-Mora, D]]~~	+
-	~~[[Category: Ortega, A]]~~	+
-	~~[[Category: Chemoreceptor]]~~	+
-	~~[[Category: Chemotaxis]]~~	+
-	~~[[Category: Nitrate~~]]	+
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]
-	[[Category: ~~Signaling protein~~]]	+	[[Category: Gavira JA]]
		+	[[Category: Krell T]]
		+	[[Category: Martin-Mora D]]
		+	[[Category: Ortega A]]

OCA at 15:58, 27 February 2019

OCA — Wed, 27 Feb 2019 15:58:28 GMT

←Older revision		Revision as of 15:58, 27 February 2019
Line 3:		Line 3:
	<StructureSection load='6gcv' size='340' side='right' caption='[[6gcv]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='6gcv' size='340' side='right' caption='[[6gcv]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6gcv]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GCV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GCV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6gcv]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GCV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GCV 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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>		</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pctC_5, pctC_1, AOY09_04118, CAZ03_12680, CAZ10_05855, PAMH19_2341, RW109_RW109_03190 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</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=6gcv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gcv OCA], [http://pdbe.org/6gcv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6gcv RCSB], [http://www.ebi.ac.uk/pdbsum/6gcv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6gcv 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=6gcv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gcv OCA], [http://pdbe.org/6gcv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6gcv RCSB], [http://www.ebi.ac.uk/pdbsum/6gcv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6gcv ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Chemotaxis and energy taxis permit directed bacterial movements in gradients of environmental cues. Nitrate is a final electron acceptor for anaerobic respiration and can also serve as a nitrogen source for aerobic growth. Previous studies indicated that bacterial nitrate taxis is mediated by energy taxis mechanisms, which are based on the cytosolic detection of consequences of nitrate metabolism. Here we show that Pseudomonas aeruginosa PAO1 mediates nitrate chemotaxis on the basis of specific nitrate sensing by the periplasmic PilJ domain of the PA2788/McpN chemoreceptor. The presence of nitrate reduced mcpN transcript levels, and McpN-mediated taxis occurred only under nitrate starvation conditions. In contrast to the NarX and NarQ sensor kinases, McpN bound nitrate specifically and showed no affinity for other ligands such as nitrite. We report the three-dimensional structure of the McpN ligand binding domain (LBD) at 1.3-A resolution in complex with nitrate. Although structurally similar to 4-helix bundle domains, the ligand binding mode differs since a single nitrate molecule is bound to a site on the dimer symmetry axis. As for 4-helix bundle domains, ligand binding stabilized the McpN-LBD dimer. McpN homologues showed a wide phylogenetic distribution, indicating that nitrate chemotaxis is a widespread phenotype. These homologues were particularly abundant in bacteria that couple sulfide/sulfur oxidation with nitrate reduction. This work expands the range of known chemotaxis effectors and forms the basis for the exploration of nitrate chemotaxis in other bacteria and for the study of its physiological role.IMPORTANCE Nitrate is of central importance in bacterial physiology. Previous studies indicated that movements toward nitrate are due to energy taxis, which is based on the cytosolic sensing of consequences of nitrate metabolism. Here we present the first report on nitrate chemotaxis. This process is initiated by specific nitrate binding to the periplasmic ligand binding domain (LBD) of McpN. Nitrate chemotaxis is highly regulated and occurred only under nitrate starvation conditions, which is helpful information to explore nitrate chemotaxis in other bacteria. We present the three-dimensional structure of the McpN-LBD in complex with nitrate, which is the first structure of a chemoreceptor PilJ-type domain. This structure reveals striking similarities to that of the abundant 4-helix bundle domain but employs a different sensing mechanism. Since McpN homologues show a wide phylogenetic distribution, nitrate chemotaxis is likely a widespread phenomenon with importance for the life cycle of ecologically diverse bacteria.
		+
		+	The Molecular Mechanism of Nitrate Chemotaxis via Direct Ligand Binding to the PilJ Domain of McpN.,Martin-Mora D, Ortega A, Matilla MA, Martinez-Rodriguez S, Gavira JA, Krell T MBio. 2019 Feb 19;10(1). pii: mBio.02334-18. doi: 10.1128/mBio.02334-18. PMID:30782655<ref>PMID:30782655</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6gcv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 19:56, 19 September 2018

OCA — Wed, 19 Sep 2018 19:56:03 GMT

←Older revision		Revision as of 19:56, 19 September 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6gcv ~~is ON HOLD until Paper Publication~~	+	==Ligand binding domain (LBD) of the p. aeruginosa nitrate receptor McpN==
-		+	<StructureSection load='6gcv' size='340' side='right' caption='[[6gcv]], [[Resolution\|resolution]] 1.30Å' scene=''>
-	~~Authors~~: ~~Gavira, J~~.A., ~~Krell~~, T., ~~Martin~~-~~Mora~~, D., ~~Ortega~~, A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6gcv]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GCV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GCV FirstGlance]. <br>
-	~~Description~~: ~~Ligand binding domain (LBD) of the p. aeruginosa nitrate receptor McpN~~	+	</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=6gcv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gcv OCA], [http://pdbe.org/6gcv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6gcv RCSB], [http://www.ebi.ac.uk/pdbsum/6gcv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6gcv ProSAT]</span></td></tr>
-	[[Category: ~~Gavira~~, ~~J.A~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Gavira, J A]]
		+	[[Category: Krell, T]]
		+	[[Category: Martin-Mora, D]]
	[[Category: Ortega, A]]		[[Category: Ortega, A]]
-	[[Category: ~~Martin-Mora, D~~]]	+	[[Category: Chemoreceptor]]
-	[[Category: ~~Krell, T~~]]	+	[[Category: Chemotaxis]]
		+	[[Category: Nitrate]]
		+	[[Category: Pseudomonas aeruginosa]]
		+	[[Category: Signaling protein]]

OCA at 06:52, 2 May 2018

OCA — Wed, 02 May 2018 06:52:29 GMT

←Older revision		Revision as of 06:52, 2 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6gcv is ON HOLD	+	The entry 6gcv is ON HOLD until Paper Publication

	Authors: Gavira, J.A., Krell, T., Martin-Mora, D., Ortega, A.		Authors: Gavira, J.A., Krell, T., Martin-Mora, D., Ortega, A.

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

OCA — Wed, 25 Apr 2018 04:23:37 GMT

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

←Older revision

Revision as of 04:23, 25 April 2018

OCA: New page: '''Unreleased structure''' The entry 6gcv is ON HOLD Authors: Gavira, J.A., Krell, T., Martin-Mora, D., Ortega, A. Description: Ligand binding domain (LBD) of the p. aeruginosa nitrate...

OCA — Wed, 25 Apr 2018 04:23:36 GMT

New page: '''Unreleased structure''' The entry 6gcv is ON HOLD Authors: Gavira, J.A., Krell, T., Martin-Mora, D., Ortega, A. Description: Ligand binding domain (LBD) of the p. aeruginosa nitrate...

New page

'''Unreleased structure'''

The entry 6gcv is ON HOLD

Authors: Gavira, J.A., Krell, T., Martin-Mora, D., Ortega, A.

Description: Ligand binding domain (LBD) of the p. aeruginosa nitrate receptor McpN
[[Category: Unreleased Structures]]
[[Category: Gavira, J.A]]
[[Category: Ortega, A]]
[[Category: Martin-Mora, D]]
[[Category: Krell, T]]