5jsd - Revision history

OCA at 09:17, 20 March 2024

2024-03-20T09:17:43Z

← Older revision		Revision as of 09:17, 20 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/A0A159BDB5_9CAUD A0A159BDB5_9CAUD]		[https://www.uniprot.org/uniprot/A0A159BDB5_9CAUD A0A159BDB5_9CAUD]
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	With an increase in antibiotic-resistant strains, the nosocomial pathogen Acinetobacter baumannii has become a serious threat to global health. Glycoconjugate vaccines containing fragments of bacterial exopolysaccharide (EPS) are an emerging therapeutic to combat bacterial infection. Herein, we characterize the bacteriophage PhiAB6 tailspike protein (TSP), which specifically hydrolyzed the EPS of A. baumannii strain 54149 (Ab-54149). Ab-54149 EPS exhibited the same chemical structure as two antibiotic-resistant A. baumannii strains. The PhiAB6 TSP-digested products comprised oligosaccharides of two repeat units, typically with stoichiometric pseudaminic acid (Pse). The 1.48-1.89-A resolution crystal structures of an N-terminally-truncated PhiAB6 TSP and its complexes with the semi-hydrolyzed products revealed a trimeric beta-helix architecture that bears intersubunit carbohydrate-binding grooves, with some features unusual to the TSP family. The structures suggest that Pse in the substrate is an important recognition site for PhiAB6 TSP. A region in the carbohydrate-binding groove is identified as the determinant of product specificity. The structures also elucidated a retaining mechanism, for which the catalytic residues were verified by site-directed mutagenesis. Our findings provide a structural basis for engineering the enzyme to produce desired oligosaccharides, which is useful for the development of glycoconjugate vaccines against A. baumannii infection.

	Structural basis for fragmenting the exopolysaccharide of Acinetobacter baumannii by bacteriophage PhiAB6 tailspike protein.,Lee IM, Tu IF, Yang FL, Ko TP, Liao JH, Lin NT, Wu CY, Ren CT, Wang AH, Chang CM, Huang KF, Wu SH Sci Rep. 2017 Feb 17;7:42711. doi: 10.1038/srep42711. PMID:28209973<ref>PMID:28209973</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 5jsd" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Tailspike protein\|Tailspike protein]]		*[[Tailspike protein 3D structures\|Tailspike protein 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 19:04, 20 September 2023

2023-09-20T19:04:25Z

← Older revision		Revision as of 19:04, 20 September 2023
Line 3:		Line 3:
	<StructureSection load='5jsd' size='340' side='right'caption='[[5jsd]], [[Resolution\|resolution]] 1.48Å' scene=''>		<StructureSection load='5jsd' size='340' side='right'caption='[[5jsd]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5jsd]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bacteriophage_sp. Bacteriophage sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JSD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JSD FirstGlance]. <br>		<table><tr><td colspan='2'>[[5jsd]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteriophage_sp. Bacteriophage sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JSD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JSD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1GN:2-DEOXY-2-AMINOGALACTOSE'>1GN</scene>, <scene name='pdbligand=6PZ:5,7-DIAMINO-2,6-ANHYDRO-3,5,7,9-TETRADEOXY-L-ERYTHRO-L-GALACTO-NONONIC+ACID'>6PZ</scene>, <scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MLA:MALONIC+ACID'>MLA</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]] 1.48Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jse\|5jse]], [[5js4\|5js4]]~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1GN:2-DEOXY-2-AMINOGALACTOSE'>1GN</scene>, <scene name='pdbligand=6PZ:5,7-DIAMINO-2,6-ANHYDRO-3,5,7,9-TETRADEOXY-L-ERYTHRO-L-GALACTO-NONONIC+ACID'>6PZ</scene>, <scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MLA:MALONIC+ACID'>MLA</scene></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=5jsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jsd OCA], [~~http~~://pdbe.org/5jsd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jsd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jsd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jsd 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=5jsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jsd OCA], [https://pdbe.org/5jsd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jsd RCSB], [https://www.ebi.ac.uk/pdbsum/5jsd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jsd ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/A0A159BDB5_9CAUD A0A159BDB5_9CAUD]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 28:
	[[Category: Bacteriophage sp]]		[[Category: Bacteriophage sp]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Huang~~, K F~~]]		[[Category: Huang KF]]
	[[Category: Lee~~, I M~~]]		[[Category: Lee IM]]
	[[Category: Tu~~, I F~~]]		[[Category: Tu IF]]
	[[Category: Wu~~, S H]]~~		[[Category: Wu SH]]
	~~[[Category: Beta-helix]]~~
	~~[[Category: Superhelical trimer]]~~
	~~[[Category: Viral protein]]~~
	~~[[Category: Viral tailspike~~]]

OCA at 11:36, 17 June 2020

2020-06-17T11:36:10Z

← Older revision		Revision as of 11:36, 17 June 2020
Line 1:		Line 1:

	==Crystal structure of phiAB6 tailspike in complex with five-repeated oligosaccharides of Acinetobacter baumannii surface polysaccharide==		==Crystal structure of phiAB6 tailspike in complex with five-repeated oligosaccharides of Acinetobacter baumannii surface polysaccharide==
	<StructureSection load='5jsd' size='340' side='right' caption='[[5jsd]], [[Resolution\|resolution]] 1.48Å' scene=''>		<StructureSection load='5jsd' size='340' side='right'caption='[[5jsd]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5jsd]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_sp. Bacteriophage sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JSD OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JSD FirstGlance]. <br>		<table><tr><td colspan='2'>[[5jsd]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_sp. Bacteriophage sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JSD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JSD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1GN:2-DEOXY-2-AMINOGALACTOSE'>1GN</scene>, <scene name='pdbligand=6PZ:5,7-DIAMINO-2,6-ANHYDRO-3,5,7,9-TETRADEOXY-L-ERYTHRO-L-GALACTO-NONONIC+ACID'>6PZ</scene>, <scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MLA:MALONIC+ACID'>MLA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1GN:2-DEOXY-2-AMINOGALACTOSE'>1GN</scene>, <scene name='pdbligand=6PZ:5,7-DIAMINO-2,6-ANHYDRO-3,5,7,9-TETRADEOXY-L-ERYTHRO-L-GALACTO-NONONIC+ACID'>6PZ</scene>, <scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MLA:MALONIC+ACID'>MLA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jse\|5jse]], [[5js4\|5js4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jse\|5jse]], [[5js4\|5js4]]</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=5jsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jsd OCA], [http://pdbe.org/5jsd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jsd RCSB], [http://www.ebi.ac.uk/pdbsum/5jsd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jsd 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=5jsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jsd OCA], [http://pdbe.org/5jsd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jsd RCSB], [http://www.ebi.ac.uk/pdbsum/5jsd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jsd ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5jsd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5jsd" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Tailspike protein\|Tailspike protein]]
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Bacteriophage sp]]		[[Category: Bacteriophage sp]]
			[[Category: Large Structures]]
	[[Category: Huang, K F]]		[[Category: Huang, K F]]
	[[Category: Lee, I M]]		[[Category: Lee, I M]]

OCA at 07:25, 29 November 2017

2017-11-29T07:25:22Z

← Older revision		Revision as of 07:25, 29 November 2017
Line 3:		Line 3:
	<StructureSection load='5jsd' size='340' side='right' caption='[[5jsd]], [[Resolution\|resolution]] 1.48Å' scene=''>		<StructureSection load='5jsd' size='340' side='right' caption='[[5jsd]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5jsd]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JSD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JSD FirstGlance]. <br>		<table><tr><td colspan='2'>[[5jsd]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_sp. Bacteriophage sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JSD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JSD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1GN:2-DEOXY-2-AMINOGALACTOSE'>1GN</scene>, <scene name='pdbligand=6PZ:5,7-DIAMINO-2,6-ANHYDRO-3,5,7,9-TETRADEOXY-L-ERYTHRO-L-GALACTO-NONONIC+ACID'>6PZ</scene>, <scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MLA:MALONIC+ACID'>MLA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1GN:2-DEOXY-2-AMINOGALACTOSE'>1GN</scene>, <scene name='pdbligand=6PZ:5,7-DIAMINO-2,6-ANHYDRO-3,5,7,9-TETRADEOXY-L-ERYTHRO-L-GALACTO-NONONIC+ACID'>6PZ</scene>, <scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MLA:MALONIC+ACID'>MLA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jse\|5jse]], [[5js4\|5js4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jse\|5jse]], [[5js4\|5js4]]</td></tr>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Bacteriophage sp]]
	[[Category: Huang, K F]]		[[Category: Huang, K F]]
	[[Category: Lee, I M]]		[[Category: Lee, I M]]

OCA at 16:44, 9 March 2017

2017-03-09T16:44:31Z

@@ Line 1: / Line 1: @@
-The entry 5jsd is ON HOLD  until Paper Publication
+==Crystal structure of phiAB6 tailspike in complex with five-repeated oligosaccharides of Acinetobacter baumannii surface polysaccharide==
-Authors:
+Structural basis for fragmenting the exopolysaccharide of Acinetobacter baumannii by bacteriophage PhiAB6 tailspike protein.,Lee IM, Tu IF, Yang FL, Ko TP, Liao JH, Lin NT, Wu CY, Ren CT, Wang AH, Chang CM, Huang KF, Wu SH Sci Rep. 2017 Feb 17;7:42711. doi: 10.1038/srep42711. PMID:28209973<ref>PMID:28209973</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>

OCA at 08:34, 14 July 2016

2016-07-14T08:34:18Z

← Older revision		Revision as of 08:34, 14 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 5jsd is ON HOLD		The entry 5jsd is ON HOLD until Paper Publication

	Authors:		Authors:

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

2016-06-01T13:46:16Z

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

← Older revision	Revision as of 13:46, 1 June 2016
(No difference)

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

2016-06-01T13:46:15Z

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

New page

'''Unreleased structure'''

The entry 5jsd is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]