6iot - Revision history

OCA at 10:34, 27 March 2024

OCA — Wed, 27 Mar 2024 10:34:28 GMT

←Older revision		Revision as of 10:34, 27 March 2024
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	<StructureSection load='6iot' size='340' side='right'caption='[[6iot]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='6iot' size='340' side='right'caption='[[6iot]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6iot]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IOT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6IOT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6iot]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IOT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IOT FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ARG:ARGININE'>ARG</scene~~>, ~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.7Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[6iop\|6iop]], [[6ioq\|6ioq]], [[6ior\|6ior]], [[6ios\|6ios]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">mcpB_4, ERS013206_02812 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=666 "Bacillo virgola del Koch" Trevisan 1884])~~</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=6iot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iot OCA], [https://pdbe.org/6iot PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6iot RCSB], [https://www.ebi.ac.uk/pdbsum/6iot PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6iot 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=6iot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iot OCA], [~~http~~://pdbe.org/6iot PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6iot RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6iot PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6iot ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q9KQ43_VIBCH Q9KQ43_VIBCH]
-	Bacteria sense environmental chemicals using chemosensor proteins, most of which are present in the cytoplasmic membrane. Canonical chemoreceptors bind their specific ligands in their periplasmic domain, and the ligand binding creates a molecular stimulus that is transmitted into the cytoplasm, leading to various cellular responses, such as chemotaxis and specific gene expression. Vibrio cholerae, the causative agent of cholera, contains about 44 putative sensor proteins, which are homologous to methyl-accepting chemotaxis proteins involved in chemotaxis. Two of them, Mlp24 and Mlp37, have been identified as chemoreceptors that mediate chemotactic responses to various amino acids. Although most of the residues of Mlp37 involved in ligand binding are conserved in Mlp24, these chemoreceptors bind the same ligands with different affinities. Moreover, they have distinct cellular roles. Here we determined a series of ligand complex structures of the periplasmic domains of Mlp24 (Mlp24p). The structures revealed that Ca(2+) binds to the loop that forms the upper wall of the ligand-binding pocket. Ca(2+) does not bind to the corresponding loop of Mlp37, implying that the structural difference of the loop may cause the ligand affinity difference. ITC measurements indicated that Ca(2+) changes the ligand binding affinity of Mlp24p. Furthermore, Ca(2+) affected chemotactic behaviors to various amino acids mediated by Mlp24. Thus, Ca(2+) is suggested to serve as a co-signal for the primary signal mediated by Mlp24p and V. cholerae fine-tunes its chemotactic behavior depending on the Ca(2+) concentration by modulating the ligand sensitivity of Mlp24.ImportanceMlp24 and Mlp37 are homologous chemoreceptors of Vibrio cholerae that bind various amino acids. Although most of the residues involved in ligand interaction are conserved, these chemoreceptors show different affinity for the same ligand and play different cellular roles. A series of ligand complex structures of the periplasmic region of Mlp24 (Mlp24p) and following ITC analysis revealed that Ca(2+) binds to the loop of Mlp24p and modulates the ligand binding affinity of Mlp24p. Moreover, Ca(2+) changes the chemotactic behaviors mediated by Mlp24. We propose that Ca(2+) acts as a co-signal that modulates the affinity of Mlp24 for the primary signal, thereby changes the chemotactic behavior of V. ~~cholerae~~.	+

-	Calcium ion modulates amino acid sensing of the chemoreceptor Mlp24 of Vibrio cholerae.,Takahashi Y, Nishiyama SI, Sumita K, Kawagishi I, Imada K J Bacteriol. 2019 Feb 11. pii: JB.00779-18. doi: 10.1128/JB.00779-18. PMID:30745373<ref>PMID:30745373</ref>	+	==See Also==
-		+	*[[Chemotaxis protein 3D structures\|Chemotaxis protein 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6iot" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillo virgola del koch trevisan 1884]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Imada, K]]	+	[[Category: Vibrio cholerae]]
-	[[Category: Kawagishi, I]]	+	[[Category: Imada K]]
-	[[Category: Nishiyama, S]]	+	[[Category: Kawagishi I]]
-	[[Category: Sumita, K]]	+	[[Category: Nishiyama S]]
-	[[Category: Takahashi, Y]]	+	[[Category: Sumita K]]
-	~~[[Category: Chemoreceptor]]~~	+	[[Category: Takahashi Y]]
-	~~[[Category: Ligand complex]]~~	+
-	~~[[Category: Mcp-like protein]]~~	+
-	~~[[Category: Pas-like domain]]~~	+
-	~~[[Category: Signaling protein~~]]	+

OCA at 08:15, 24 April 2019

OCA — Wed, 24 Apr 2019 08:15:02 GMT

←Older revision		Revision as of 08:15, 24 April 2019
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	<StructureSection load='6iot' size='340' side='right'caption='[[6iot]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='6iot' size='340' side='right'caption='[[6iot]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6iot]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IOT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IOT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6iot]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IOT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IOT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6iop\|6iop]], [[6ioq\|6ioq]], [[6ior\|6ior]], [[6ios\|6ios]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6iop\|6iop]], [[6ioq\|6ioq]], [[6ior\|6ior]], [[6ios\|6ios]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mcpB_4, ERS013206_02812 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=666 "Bacillo virgola del Koch" Trevisan 1884])</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=6iot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iot OCA], [http://pdbe.org/6iot PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iot RCSB], [http://www.ebi.ac.uk/pdbsum/6iot PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iot 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=6iot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iot OCA], [http://pdbe.org/6iot PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iot RCSB], [http://www.ebi.ac.uk/pdbsum/6iot PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iot ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillo virgola del koch trevisan 1884]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Imada, K]]		[[Category: Imada, K]]

OCA at 07:58, 20 March 2019

OCA — Wed, 20 Mar 2019 07:58:54 GMT

←Older revision		Revision as of 07:58, 20 March 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 6iot is ~~ON HOLD~~	+	==The ligand binding domain of Mlp24 with arginine==
		+	<StructureSection load='6iot' size='340' side='right'caption='[[6iot]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6iot]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IOT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IOT FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6iop\|6iop]], [[6ioq\|6ioq]], [[6ior\|6ior]], [[6ios\|6ios]]</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=6iot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iot OCA], [http://pdbe.org/6iot PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iot RCSB], [http://www.ebi.ac.uk/pdbsum/6iot PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iot ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacteria sense environmental chemicals using chemosensor proteins, most of which are present in the cytoplasmic membrane. Canonical chemoreceptors bind their specific ligands in their periplasmic domain, and the ligand binding creates a molecular stimulus that is transmitted into the cytoplasm, leading to various cellular responses, such as chemotaxis and specific gene expression. Vibrio cholerae, the causative agent of cholera, contains about 44 putative sensor proteins, which are homologous to methyl-accepting chemotaxis proteins involved in chemotaxis. Two of them, Mlp24 and Mlp37, have been identified as chemoreceptors that mediate chemotactic responses to various amino acids. Although most of the residues of Mlp37 involved in ligand binding are conserved in Mlp24, these chemoreceptors bind the same ligands with different affinities. Moreover, they have distinct cellular roles. Here we determined a series of ligand complex structures of the periplasmic domains of Mlp24 (Mlp24p). The structures revealed that Ca(2+) binds to the loop that forms the upper wall of the ligand-binding pocket. Ca(2+) does not bind to the corresponding loop of Mlp37, implying that the structural difference of the loop may cause the ligand affinity difference. ITC measurements indicated that Ca(2+) changes the ligand binding affinity of Mlp24p. Furthermore, Ca(2+) affected chemotactic behaviors to various amino acids mediated by Mlp24. Thus, Ca(2+) is suggested to serve as a co-signal for the primary signal mediated by Mlp24p and V. cholerae fine-tunes its chemotactic behavior depending on the Ca(2+) concentration by modulating the ligand sensitivity of Mlp24.ImportanceMlp24 and Mlp37 are homologous chemoreceptors of Vibrio cholerae that bind various amino acids. Although most of the residues involved in ligand interaction are conserved, these chemoreceptors show different affinity for the same ligand and play different cellular roles. A series of ligand complex structures of the periplasmic region of Mlp24 (Mlp24p) and following ITC analysis revealed that Ca(2+) binds to the loop of Mlp24p and modulates the ligand binding affinity of Mlp24p. Moreover, Ca(2+) changes the chemotactic behaviors mediated by Mlp24. We propose that Ca(2+) acts as a co-signal that modulates the affinity of Mlp24 for the primary signal, thereby changes the chemotactic behavior of V. cholerae.

-	~~Authors: Takahashi~~, Y., ~~Sumita~~, K~~., Nishiyama, S.~~, Kawagishi, I., Imada, K.	+	Calcium ion modulates amino acid sensing of the chemoreceptor Mlp24 of Vibrio cholerae.,Takahashi Y, Nishiyama SI, Sumita K, Kawagishi I, Imada K J Bacteriol. 2019 Feb 11. pii: JB.00779-18. doi: 10.1128/JB.00779-18. PMID:30745373<ref>PMID:30745373</ref>

-	~~Description: The ligand binding domain~~ of ~~Mlp24 with arginine~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Sumita, K]]~~	+	<div class="pdbe-citations 6iot" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Kawagishi, I~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Imada, K]]		[[Category: Imada, K]]
-	[[Category: ~~Takahashi~~, Y]]	+	[[Category: Kawagishi, I]]
	[[Category: Nishiyama, S]]		[[Category: Nishiyama, S]]
		+	[[Category: Sumita, K]]
		+	[[Category: Takahashi, Y]]
		+	[[Category: Chemoreceptor]]
		+	[[Category: Ligand complex]]
		+	[[Category: Mcp-like protein]]
		+	[[Category: Pas-like domain]]
		+	[[Category: Signaling protein]]

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

OCA — Wed, 07 Nov 2018 10:45:24 GMT

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

←Older revision

Revision as of 10:45, 7 November 2018

OCA: New page: '''Unreleased structure''' The entry 6iot is ON HOLD Authors: Takahashi, Y., Sumita, K., Nishiyama, S., Kawagishi, I., Imada, K. Description: The ligand binding domain of Mlp24 with ar...

OCA — Wed, 07 Nov 2018 10:45:23 GMT

New page: '''Unreleased structure''' The entry 6iot is ON HOLD Authors: Takahashi, Y., Sumita, K., Nishiyama, S., Kawagishi, I., Imada, K. Description: The ligand binding domain of Mlp24 with ar...

New page

'''Unreleased structure'''

The entry 6iot is ON HOLD

Authors: Takahashi, Y., Sumita, K., Nishiyama, S., Kawagishi, I., Imada, K.

Description: The ligand binding domain of Mlp24 with arginine
[[Category: Unreleased Structures]]
[[Category: Sumita, K]]
[[Category: Kawagishi, I]]
[[Category: Imada, K]]
[[Category: Takahashi, Y]]
[[Category: Nishiyama, S]]