7vev - Revision history

OCA at 17:24, 29 November 2023

2023-11-29T17:24:00Z

←Older revision		Revision as of 17:24, 29 November 2023
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	==Crystal structure of bacterial chemotaxis-dependent pectin-binding protein SPH1118 in complex with MES==		==Crystal structure of bacterial chemotaxis-dependent pectin-binding protein SPH1118 in complex with MES==
-	<StructureSection load='7vev' size='340' side='right'caption='[[7vev]]' scene=''>	+	<StructureSection load='7vev' size='340' side='right'caption='[[7vev]], [[Resolution\|resolution]] 1.50Å' 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=7VEV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VEV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7vev]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_sp._A1 Sphingomonas sp. A1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VEV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VEV FirstGlance]. <br>
-	</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=7vev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vev OCA], [https://pdbe.org/7vev PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vev RCSB], [https://www.ebi.ac.uk/pdbsum/7vev PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vev ProSAT]</span></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]] 1.498Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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=7vev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vev OCA], [https://pdbe.org/7vev PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vev RCSB], [https://www.ebi.ac.uk/pdbsum/7vev PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vev ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Gram-negative Sphingomonas sp. strain A1 exhibits positive chemotaxis toward acidic polysaccharide pectin. SPH1118 has been identified as a pectin-binding protein involved in both pectin chemotaxis and assimilation. Here we show tertiary structures of SPH1118 with six different conformations as determined by X-ray crystallography. SPH1118 consisted of two domains with a large cleft between the domains and substrates bound to positively charged and aromatic residues in the cleft through hydrogen bond and stacking interactions. Substrate-free SPH1118 adopted three different conformations in the open form. On the other hand, the two domains were closed in substrate-bound form and the domain closure ratio was changed in response to the substrate size, suggesting that the conformational change upon binding to the substrate triggered the expression of pectin chemotaxis and assimilation. This study first clarified that the solute-binding protein with dual functions recognized the substrate through flexible conformational changes in response to the substrate size.
		+
		+	Substrate size-dependent conformational changes of bacterial pectin-binding protein crucial for chemotaxis and assimilation.,Anamizu K, Takase R, Hio M, Watanabe D, Mikami B, Hashimoto W Sci Rep. 2022 Jul 25;12(1):12653. doi: 10.1038/s41598-022-16540-5. PMID:35879323<ref>PMID:35879323</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7vev" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Sphingomonas sp. A1]]
	[[Category: Anamizu K]]		[[Category: Anamizu K]]
	[[Category: Hashimoto W]]		[[Category: Hashimoto W]]

OCA at 06:22, 18 August 2022

2022-08-18T06:22:33Z

←Older revision		Revision as of 06:22, 18 August 2022
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-	'''Unreleased structure'''

-	~~The entry 7vev is ON HOLD until Paper Publication~~	+	==Crystal structure of bacterial chemotaxis-dependent pectin-binding protein SPH1118 in complex with MES==
-		+	<StructureSection load='7vev' size='340' side='right'caption='[[7vev]]' scene=''>
-	~~Authors: Anamizu, K., Takase, R., Hio, M., Watanebe, D., Mikami, B., Hashimoto, W.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VEV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VEV FirstGlance]. <br>
-	~~Description:~~ Crystal structure of bacterial chemotaxis-dependent pectin-binding protein SPH1118 in complex with MES	+	</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=7vev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vev OCA], [https://pdbe.org/7vev PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vev RCSB], [https://www.ebi.ac.uk/pdbsum/7vev PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vev ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Hio~~, M]]	+	__TOC__
-	[[Category: ~~Takase, R~~]]	+	</StructureSection>
-	[[Category: ~~Watanebe, D~~]]	+	[[Category: Large Structures]]
-	[[Category: Hashimoto, W]]	+	[[Category: Anamizu K]]
-	[[Category: Mikami, B]]	+	[[Category: Hashimoto W]]
-	[[Category: ~~Anamizu, K~~]]	+	[[Category: Hio M]]
		+	[[Category: Mikami B]]
		+	[[Category: Takase R]]
		+	[[Category: Watanebe D]]

OCA at 10:31, 13 October 2021

2021-10-13T10:31:18Z

←Older revision		Revision as of 10:31, 13 October 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7vev is ON HOLD	+	The entry 7vev is ON HOLD until Paper Publication

	Authors: Anamizu, K., Takase, R., Hio, M., Watanebe, D., Mikami, B., Hashimoto, W.		Authors: Anamizu, K., Takase, R., Hio, M., Watanebe, D., Mikami, B., Hashimoto, W.

OCA: Protected "7vev" [edit=sysop:move=sysop]

2021-09-15T08:29:41Z

Protected "7vev" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:29, 15 September 2021

OCA: New page: '''Unreleased structure''' The entry 7vev is ON HOLD Authors: Anamizu, K., Takase, R., Hio, M., Watanebe, D., Mikami, B., Hashimoto, W. Description: Crystal structure of bacterial chem...

2021-09-15T08:29:40Z

New page: '''Unreleased structure''' The entry 7vev is ON HOLD Authors: Anamizu, K., Takase, R., Hio, M., Watanebe, D., Mikami, B., Hashimoto, W. Description: Crystal structure of bacterial chem...

New page

'''Unreleased structure'''

The entry 7vev is ON HOLD

Authors: Anamizu, K., Takase, R., Hio, M., Watanebe, D., Mikami, B., Hashimoto, W.

Description: Crystal structure of bacterial chemotaxis-dependent pectin-binding protein SPH1118 in complex with MES
[[Category: Unreleased Structures]]
[[Category: Hio, M]]
[[Category: Takase, R]]
[[Category: Watanebe, D]]
[[Category: Hashimoto, W]]
[[Category: Mikami, B]]
[[Category: Anamizu, K]]