5gub - Revision history

OCA at 11:42, 2 August 2023

2023-08-02T11:42:45Z

←Older revision		Revision as of 11:42, 2 August 2023
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	<StructureSection load='5gub' size='340' side='right'caption='[[5gub]], [[Resolution\|resolution]] 1.78Å' scene=''>		<StructureSection load='5gub' size='340' side='right'caption='[[5gub]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gub]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5GUB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gub]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptobacillus_moniliformis_DSM_12112 Streptobacillus moniliformis DSM 12112]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GUB 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</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]] 1.78Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5gub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gub OCA], [~~http~~://pdbe.org/5gub PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5gub RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5gub PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5gub ProSAT]</span></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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene>, <scene name='pdbligand=PRD_900058:UNSATURATED+CHONDROITIN+DISACCHARIDE'>PRD_900058</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=5gub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gub OCA], [https://pdbe.org/5gub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gub RCSB], [https://www.ebi.ac.uk/pdbsum/5gub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gub ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D1AWE0_STRM9 D1AWE0_STRM9]
	<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: Hashimoto, W]]	+	[[Category: Streptobacillus moniliformis DSM 12112]]
-	[[Category: Mikami, B]]	+	[[Category: Hashimoto W]]
-	[[Category: Murata, K]]	+	[[Category: Mikami B]]
-	[[Category: Oiki, S]]	+	[[Category: Murata K]]
-	~~[[Category: Abc transporter]]~~	+	[[Category: Oiki S]]
-	~~[[Category: Glycosaminoglycan]]~~	+
-	~~[[Category: Solute-binding protein]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 06:43, 20 May 2020

2020-05-20T06:43:35Z

←Older revision		Revision as of 06:43, 20 May 2020
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	==Crystal structure of solute-binding protein complexed with sulfate group-free unsaturated chondroitin disaccharide==		==Crystal structure of solute-binding protein complexed with sulfate group-free unsaturated chondroitin disaccharide==
-	<StructureSection load='5gub' size='340' side='right' caption='[[5gub]], [[Resolution\|resolution]] 1.78Å' scene=''>	+	<StructureSection load='5gub' size='340' side='right'caption='[[5gub]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gub]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUB OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GUB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gub]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GUB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene></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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</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=5gub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gub OCA], [http://pdbe.org/5gub PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gub RCSB], [http://www.ebi.ac.uk/pdbsum/5gub PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gub ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5gub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gub OCA], [http://pdbe.org/5gub PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gub RCSB], [http://www.ebi.ac.uk/pdbsum/5gub PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gub ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Hashimoto, W]]		[[Category: Hashimoto, W]]
	[[Category: Mikami, B]]		[[Category: Mikami, B]]

OCA at 15:59, 20 October 2017

2017-10-20T15:59:07Z

←Older revision		Revision as of 15:59, 20 October 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5gub is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of solute-binding protein complexed with sulfate group-free unsaturated chondroitin disaccharide==
		+	<StructureSection load='5gub' size='340' side='right' caption='[[5gub]], [[Resolution\|resolution]] 1.78Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5gub]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GUB FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</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=5gub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gub OCA], [http://pdbe.org/5gub PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gub RCSB], [http://www.ebi.ac.uk/pdbsum/5gub PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gub ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glycosaminoglycans (GAGs), such as hyaluronan, chondroitin sulfate, and heparin, constitute mammalian extracellular matrices. The uronate and amino sugar residues in hyaluronan and chondroitin sulfate are linked by 1,3-glycoside bond, while heparin contains 1,4-glycoside bond. Some bacteria target GAGs as means of establishing colonization and/or infection, and bacterial degradation mechanisms of GAGs have been well characterized. However, little is known about the bacterial import of GAGs. Here, we show a GAG import system, comprised of a solute-binding protein (Smon0123)-dependent ATP-binding cassette (ABC) transporter, in the pathogenic Streptobacillus moniliformis. A genetic cluster responsible for depolymerization, degradation, and metabolism of GAGs as well as the ABC transporter system was found in the S. moniliformis genome. This bacterium degraded hyaluronan and chondroitin sulfate with an expression of the genetic cluster, while heparin repressed the bacterial growth. The purified recombinant Smon0123 exhibited an affinity with disaccharides generated from hyaluronan and chondroitin sulfate. X-ray crystallography indicated binding mode of Smon0123 to GAG disaccharides. The purified recombinant ABC transporter as a tetramer (Smon0121-Smon0122/Smon0120-Smon0120) reconstructed in liposomes enhanced its ATPase activity in the presence of Smon0123 and GAG disaccharides. This is the first report that has molecularly depicted a bacterial import system of both sulfated and non-sulfated GAGs.

-	~~Authors~~:	+	A bacterial ABC transporter enables import of mammalian host glycosaminoglycans.,Oiki S, Mikami B, Maruyama Y, Murata K, Hashimoto W Sci Rep. 2017 Apr 21;7(1):1069. doi: 10.1038/s41598-017-00917-y. PMID:28432302<ref>PMID:28432302</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5gub" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hashimoto, W]]
		+	[[Category: Mikami, B]]
		+	[[Category: Murata, K]]
		+	[[Category: Oiki, S]]
		+	[[Category: Abc transporter]]
		+	[[Category: Glycosaminoglycan]]
		+	[[Category: Solute-binding protein]]
		+	[[Category: Sugar binding protein]]

OCA at 12:58, 26 October 2016

2016-10-26T12:58:04Z

←Older revision		Revision as of 12:58, 26 October 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

OCA at 11:47, 19 October 2016

2016-10-19T11:47:23Z

←Older revision		Revision as of 11:47, 19 October 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5gub is ON HOLD ~~until Paper Publication~~	+	The entry 5gub is ON HOLD

	Authors:		Authors:

OCA at 11:25, 3 October 2016

2016-10-03T11:25:48Z

←Older revision		Revision as of 11:25, 3 October 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2016-09-09T12:05:20Z

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

←Older revision

Revision as of 12:05, 9 September 2016

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

2016-09-09T12:05:19Z

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

New page

'''Unreleased structure'''

The entry 5gub is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]