6nw9 - Revision history

OCA at 14:49, 13 March 2024

OCA — Wed, 13 Mar 2024 14:49:12 GMT

←Older revision		Revision as of 14:49, 13 March 2024
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	<StructureSection load='6nw9' size='340' side='right'caption='[[6nw9]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='6nw9' size='340' side='right'caption='[[6nw9]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nw9]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Escherichia_phage_cba120~~ Escherichia ~~phage cba120~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NW9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6NW9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nw9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_CBA120 Escherichia virus CBA120]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NW9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NW9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.85Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5w6f\|5w6f]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">orf212 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1987159 Escherichia phage Cba120])</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=6nw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nw9 OCA], [https://pdbe.org/6nw9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nw9 RCSB], [https://www.ebi.ac.uk/pdbsum/6nw9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nw9 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=6nw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nw9 OCA], [~~http~~://pdbe.org/6nw9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6nw9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6nw9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6nw9 ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/G3M191_9CAUD G3M191_9CAUD]
-	~~Bacteriophage tailspike proteins mediate virion absorption through reversible primary receptor binding, followed by lipopolysaccharide or exopolysaccharide degradation. The Escherichia coli O157~~:~~H7 bacteriophage CBA120 genome encodes four distinct tailspike proteins, annotated as ORFs 210 through 213~~. ~~Previously, we reported the crystal structure of ORF210 (TSP1)~~. Here we describe the crystal structure of ORF212 (TSP3) determined at 1.85 A resolution. As observed with other tailspike proteins, TSP3 assembles into a trimer. Each subunit of TSP3 has an N-terminal head domain that is structurally similar to that of TSP1, consistent with their high amino acid sequence identity. In contrast, despite sharing a beta-helix fold, the overall structure of the C-terminal catalytic domain of TSP3 is quite different when compared to TSP1. The TSP3 structure suggests that the glycosidase active site resides in a cleft at the interface between two adjacent subunits where three acidic residues, Glu362 and Asp383 on one subunit, and Asp426 on a second subunit, are located in close proximity. Comparing the glycosidase activity of wild-type TSP3 to various point mutants revealed that catalysis requires the carboxyl groups of Glu362 and Asp426, and not of Asp383, confirming the enzyme employs two carboxyl groups to degrade lippopolysaccharide using an acid/~~base mechanism.~~	+

-	Structure and tailspike glycosidase machinery of ORF212 from E. coli O157:H7 phage CBA120 (TSP3).,Greenfield J, Shang X, Luo H, Zhou Y, Heselpoth RD, Nelson DC, Herzberg O Sci Rep. 2019 May 14;9(1):7349. doi: 10.1038/s41598-019-43748-9. PMID:31089181<ref>PMID:31089181</ref>	+	==See Also==
-		+	*[[Tailspike protein 3D structures\|Tailspike protein 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6nw9" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Escherichia ~~phage cba120~~]]	+	[[Category: Escherichia virus CBA120]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Greenfield~~, J Y~~]]	+	[[Category: Greenfield JY]]
-	[[Category: Herzberg, O]]	+	[[Category: Herzberg O]]
-	~~[[Category: Bacterial polysaccharide]]~~	+
-	~~[[Category: Parallel beta helix]]~~	+
-	~~[[Category: Phage cba120]]~~	+
-	~~[[Category: Phage tail]]~~	+
-	~~[[Category: Putative endo-glycosidase]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 11:46, 18 December 2019

OCA — Wed, 18 Dec 2019 11:46:51 GMT

←Older revision		Revision as of 11:46, 18 December 2019
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	<StructureSection load='6nw9' size='340' side='right'caption='[[6nw9]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='6nw9' size='340' side='right'caption='[[6nw9]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nw9]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NW9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NW9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nw9]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_phage_cba120 Escherichia phage cba120]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NW9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NW9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5w6f\|5w6f]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5w6f\|5w6f]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">orf212 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1987159 Escherichia phage Cba120])</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=6nw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nw9 OCA], [http://pdbe.org/6nw9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nw9 RCSB], [http://www.ebi.ac.uk/pdbsum/6nw9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nw9 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=6nw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nw9 OCA], [http://pdbe.org/6nw9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nw9 RCSB], [http://www.ebi.ac.uk/pdbsum/6nw9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nw9 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia phage cba120]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Greenfield, J Y]]		[[Category: Greenfield, J Y]]

OCA at 22:50, 5 June 2019

OCA — Wed, 05 Jun 2019 22:50:09 GMT

←Older revision		Revision as of 22:50, 5 June 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6nw9 is ~~ON HOLD until Paper~~ Publication	+	==CRYSTAL STRUCTURE OF A TAILSPIKE PROTEIN 3 (TSP3, ORF212) FROM ESCHERICHIA COLI O157:H7 BACTERIOPHAGE CBA120==
		+	<StructureSection load='6nw9' size='340' side='right'caption='[[6nw9]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6nw9]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NW9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NW9 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5w6f\|5w6f]]</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=6nw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nw9 OCA], [http://pdbe.org/6nw9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nw9 RCSB], [http://www.ebi.ac.uk/pdbsum/6nw9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nw9 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacteriophage tailspike proteins mediate virion absorption through reversible primary receptor binding, followed by lipopolysaccharide or exopolysaccharide degradation. The Escherichia coli O157:H7 bacteriophage CBA120 genome encodes four distinct tailspike proteins, annotated as ORFs 210 through 213. Previously, we reported the crystal structure of ORF210 (TSP1). Here we describe the crystal structure of ORF212 (TSP3) determined at 1.85 A resolution. As observed with other tailspike proteins, TSP3 assembles into a trimer. Each subunit of TSP3 has an N-terminal head domain that is structurally similar to that of TSP1, consistent with their high amino acid sequence identity. In contrast, despite sharing a beta-helix fold, the overall structure of the C-terminal catalytic domain of TSP3 is quite different when compared to TSP1. The TSP3 structure suggests that the glycosidase active site resides in a cleft at the interface between two adjacent subunits where three acidic residues, Glu362 and Asp383 on one subunit, and Asp426 on a second subunit, are located in close proximity. Comparing the glycosidase activity of wild-type TSP3 to various point mutants revealed that catalysis requires the carboxyl groups of Glu362 and Asp426, and not of Asp383, confirming the enzyme employs two carboxyl groups to degrade lippopolysaccharide using an acid/base mechanism.

-	~~Authors~~:	+	Structure and tailspike glycosidase machinery of ORF212 from E. coli O157:H7 phage CBA120 (TSP3).,Greenfield J, Shang X, Luo H, Zhou Y, Heselpoth RD, Nelson DC, Herzberg O Sci Rep. 2019 May 14;9(1):7349. doi: 10.1038/s41598-019-43748-9. PMID:31089181<ref>PMID:31089181</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6nw9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Greenfield, J Y]]
		+	[[Category: Herzberg, O]]
		+	[[Category: Bacterial polysaccharide]]
		+	[[Category: Parallel beta helix]]
		+	[[Category: Phage cba120]]
		+	[[Category: Phage tail]]
		+	[[Category: Putative endo-glycosidase]]
		+	[[Category: Viral protein]]

OCA at 05:37, 6 March 2019

OCA — Wed, 06 Mar 2019 05:37:09 GMT

←Older revision		Revision as of 05:37, 6 March 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6nw9 is ON HOLD	+	The entry 6nw9 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6nw9" [edit=sysop:move=sysop]

OCA — Wed, 13 Feb 2019 07:51:46 GMT

Protected "6nw9" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:51, 13 February 2019

OCA: New page: '''Unreleased structure''' The entry 6nw9 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 13 Feb 2019 07:51:45 GMT

New page: '''Unreleased structure''' The entry 6nw9 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6nw9 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]