6lzu - Revision history

OCA at 15:06, 29 November 2023

OCA — Wed, 29 Nov 2023 15:06:41 GMT

←Older revision		Revision as of 15:06, 29 November 2023
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	<StructureSection load='6lzu' size='340' side='right'caption='[[6lzu]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='6lzu' size='340' side='right'caption='[[6lzu]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6lzu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Vibh1 Vibh1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LZU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lzu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_harveyi_1DA3 Vibrio harveyi 1DA3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LZU FirstGlance]. <br>
-	</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 1.9Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VME_26970 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=673519 VIBH1])~~</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=6lzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lzu OCA], [https://pdbe.org/6lzu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lzu RCSB], [https://www.ebi.ac.uk/pdbsum/6lzu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lzu 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=6lzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lzu OCA], [https://pdbe.org/6lzu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lzu RCSB], [https://www.ebi.ac.uk/pdbsum/6lzu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lzu ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D0XC84_VIBH1 D0XC84_VIBH1]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Vibh1~~]]	+	[[Category: Vibrio harveyi 1DA3]]
-	[[Category: Kitaoku, Y]]	+	[[Category: Kitaoku Y]]
-	[[Category: Robinson~~, R C~~]]	+	[[Category: Robinson RC]]
-	[[Category: Suginta, W]]	+	[[Category: Suginta W]]
-	[[Category: Tran~~, L T~~]]	+	[[Category: Tran LT]]
-	[[Category: Ubonbal, P]]	+	[[Category: Ubonbal P]]
-	~~[[Category: Chitin]]~~	+
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Periplasmic solute-binding protein]]~~	+
-	~~[[Category: Sugar binding protein]]~~	+
-	~~[[Category: Vibrio~~]]	+

OCA at 09:02, 8 September 2021

OCA — Wed, 08 Sep 2021 09:02:40 GMT

←Older revision		Revision as of 09:02, 8 September 2021
Line 1:		Line 1:

	==F411A mutant of chitin-specific solute binding protein from Vibrio harveyi co-crystalized with chitobiose.==		==F411A mutant of chitin-specific solute binding protein from Vibrio harveyi co-crystalized with chitobiose.==
-	<StructureSection load='6lzu' size='340' side='right'caption='[[6lzu]]' scene=''>	+	<StructureSection load='6lzu' size='340' side='right'caption='[[6lzu]], [[Resolution\|resolution]] 1.90Å' 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=6LZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LZU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lzu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibh1 Vibh1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LZU 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=6lzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lzu OCA], [https://pdbe.org/6lzu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lzu RCSB], [https://www.ebi.ac.uk/pdbsum/6lzu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lzu 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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VME_26970 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=673519 VIBH1])</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=6lzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lzu OCA], [https://pdbe.org/6lzu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lzu RCSB], [https://www.ebi.ac.uk/pdbsum/6lzu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lzu ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	VhCBP is a periplasmic chitooligo saccharide-specific binding protein mainly responsible for translocation of the chitooligosaccharide (GlcNAc)2 across the double membranes of marine bacteria Vibrio harveyi. However, structural and thermodynamic understanding of the sugar binding/release processes of VhCBP are relatively unknown. VhCBP displayed the greatest affinity towards (GlcNAc)2, with lower affinity for longer-chain chitooligosaccharides [(GlcNAc)3-4]. (GlcNAc)4 partially occupied the closed sugar-binding groove, with two reducing-end GlcNAc units extending beyond the sugar-binding groove and barely characterized by weak electron density. Mutation of three conserved residues (Trp(363), Asp(365) and Trp(513)) to Ala resulted in drastic decreases in the binding affinity towards the preferred substrate (GlcNAc)2, indicating their significant contributions to sugar binding. The structure of the W513A-(GlcNAc)2 complex in a 'half-open' conformation unveiled the intermediary step of the (GlcNAc)2 translocation from the soluble CBP in periplasm to the inner membrane-transporting components. Isothermal calorimetry data suggested that VhCBP adopts the high affinity conformation to bind (GlcNAc)2, whilst its low affinity conformation facilitated sugar release. Thus, chitooligosaccharide translocation, conferred by periplasmic VhCBP, is a crucial step in the chitin catabolic pathway, allowing Vibrio bacteria to thrive in oceans where chitin is their major source of nutrients.
		+
		+	A structural model for (GlcNAc)2 translocation via a periplasmic chitooligosaccharide binding protein from marine Vibrio bacteria.,Kitaoku Y, Fukamizo T, Kumsaoad S, Ubonbal P, Robinson RC, Suginta W J Biol Chem. 2021 Aug 13:101071. doi: 10.1016/j.jbc.2021.101071. PMID:34400168<ref>PMID:34400168</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6lzu" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kitaoku Y]]	+	[[Category: Vibh1]]
-	[[Category: Robinson RC]]	+	[[Category: Kitaoku, Y]]
-	[[Category: Suginta W]]	+	[[Category: Robinson, R C]]
-	[[Category: Tran LT]]	+	[[Category: Suginta, W]]
-	[[Category: Ubonbal P]]	+	[[Category: Tran, L T]]
		+	[[Category: Ubonbal, P]]
		+	[[Category: Chitin]]
		+	[[Category: Complex]]
		+	[[Category: Periplasmic solute-binding protein]]
		+	[[Category: Sugar binding protein]]
		+	[[Category: Vibrio]]

OCA at 06:38, 24 February 2021

OCA — Wed, 24 Feb 2021 06:38:17 GMT

←Older revision		Revision as of 06:38, 24 February 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 6lzu is ~~ON HOLD until Paper Publication~~	+	==F411A mutant of chitin-specific solute binding protein from Vibrio harveyi co-crystalized with chitobiose.==
-		+	<StructureSection load='6lzu' size='340' side='right'caption='[[6lzu]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LZU FirstGlance]. <br>
-	~~Description~~:	+	</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=6lzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lzu OCA], [https://pdbe.org/6lzu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lzu RCSB], [https://www.ebi.ac.uk/pdbsum/6lzu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lzu ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Kitaoku Y]]
		+	[[Category: Robinson RC]]
		+	[[Category: Suginta W]]
		+	[[Category: Tran LT]]
		+	[[Category: Ubonbal P]]

OCA at 08:16, 18 March 2020

OCA — Wed, 18 Mar 2020 08:16:05 GMT

←Older revision		Revision as of 08:16, 18 March 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 26 Feb 2020 08:03:01 GMT

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

←Older revision

Revision as of 08:03, 26 February 2020

OCA: New page: '''Unreleased structure''' The entry 6lzu is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 26 Feb 2020 08:02:59 GMT

New page: '''Unreleased structure''' The entry 6lzu is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6lzu is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]