6au1 - Revision history

OCA at 14:24, 4 October 2023

OCA — Wed, 04 Oct 2023 14:24:59 GMT

←Older revision		Revision as of 14:24, 4 October 2023
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	<StructureSection load='6au1' size='340' side='right'caption='[[6au1]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='6au1' size='340' side='right'caption='[[6au1]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6au1]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Alcaligenes_bronchisepticus Alcaligenes bronchisepticus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AU1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6AU1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6au1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bordetella_bronchiseptica_RB50 Bordetella bronchiseptica RB50]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AU1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AU1 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.76Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hmsF, BB1768, PgaB (BpsB,HmsF) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=257310 Alcaligenes bronchisepticus])</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6au1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6au1 OCA], [~~http~~://pdbe.org/6au1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6au1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6au1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6au1 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=6au1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6au1 OCA], [https://pdbe.org/6au1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6au1 RCSB], [https://www.ebi.ac.uk/pdbsum/6au1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6au1 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0H3LKK6_BORBR A0A0H3LKK6_BORBR]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Alcaligenes bronchisepticus~~]]	+	[[Category: Bordetella bronchiseptica RB50]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bamford~~, N C~~]]	+	[[Category: Bamford NC]]
-	[[Category: Howell~~, P L~~]]	+	[[Category: Howell PL]]
-	[[Category: Little~~, D J]]~~	+	[[Category: Little DJ]]
-	~~[[Category: Biofilm]]~~	+
-	~~[[Category: Deacetylase]]~~	+
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Pnag~~]]	+

OCA at 08:31, 8 January 2020

OCA — Wed, 08 Jan 2020 08:31:54 GMT

←Older revision		Revision as of 08:31, 8 January 2020
Line 1:		Line 1:

	==Structure of the PgaB (BpsB) glycoside hydrolase domain from Bordetella bronchiseptica==		==Structure of the PgaB (BpsB) glycoside hydrolase domain from Bordetella bronchiseptica==
-	<StructureSection load='6au1' size='340' side='right' caption='[[6au1]], [[Resolution\|resolution]] 1.76Å' scene=''>	+	<StructureSection load='6au1' size='340' side='right'caption='[[6au1]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6au1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_bronchisepticus Alcaligenes bronchisepticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AU1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AU1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6au1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_bronchisepticus Alcaligenes bronchisepticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AU1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AU1 FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Alcaligenes bronchisepticus]]		[[Category: Alcaligenes bronchisepticus]]
		+	[[Category: Large Structures]]
	[[Category: Bamford, N C]]		[[Category: Bamford, N C]]
	[[Category: Howell, P L]]		[[Category: Howell, P L]]

OCA at 05:56, 16 May 2018

OCA — Wed, 16 May 2018 05:56:36 GMT

←Older revision		Revision as of 05:56, 16 May 2018
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	<StructureSection load='6au1' size='340' side='right' caption='[[6au1]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='6au1' size='340' side='right' caption='[[6au1]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6au1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AU1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AU1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6au1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_bronchisepticus Alcaligenes bronchisepticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AU1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AU1 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hmsF, BB1768, PgaB (BpsB,HmsF) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=257310 Alcaligenes bronchisepticus])</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=6au1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6au1 OCA], [http://pdbe.org/6au1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6au1 RCSB], [http://www.ebi.ac.uk/pdbsum/6au1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6au1 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=6au1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6au1 OCA], [http://pdbe.org/6au1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6au1 RCSB], [http://www.ebi.ac.uk/pdbsum/6au1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6au1 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Poly-beta(1,6)-N-acetyl-D-glucosamine (PNAG) is a major biofilm component of many pathogenic bacteria. The production, modification, and export of PNAG in Escherichia coli and Bordetella species require the protein products encoded by the pgaABCD operon. PgaB is a two-domain periplasmic protein that contains an N-terminal deacetylase domain and a C-terminal PNAG binding domain that is critical for export. However, the exact function of the PgaB C-terminal domain remains unclear. Herein, we show that the C-terminal domains of Bordetella bronchiseptica PgaB (PgaBBb) and E. coli PgaB (PgaBEc) function as glycoside hydrolases. These enzymes hydrolyze purified deacetylated PNAG (dPNAG) from Staphylococcus aureus, disrupt PNAG-dependent biofilms formed by Bordetella pertussis, Staphylococcus carnosus, Staphylococcus epidermidis, and E. coli, and potentiate bacterial killing by gentamicin. Furthermore, we found that PgaBBb was only able to hydrolyze PNAG produced in situ by the E. coli PgaCD synthase complex when an active deacetylase domain was present. Mass spectrometry analysis of the PgaB-hydrolyzed dPNAG substrate showed a GlcN-GlcNAc-GlcNAc motif at the new reducing end of detected fragments. Our 1.76 A structure of the C-terminal domain of PgaBBb reveals a central cavity within an elongated surface groove that appears ideally suited to recognize the GlcN-GlcNAc-GlcNAc motif. The structure, in conjunction with molecular modeling and site directed mutagenesis led to the identification of the dPNAG binding subsites and D474 as the probable catalytic acid. This work expands the role of PgaB within the PNAG biosynthesis machinery, defines a new glycoside hydrolase family GH153, and identifies PgaB as a possible therapeutic agent for treating PNAG-dependent biofilm infections.
		+
		+	PgaB orthologues contain a glycoside hydrolase domain that cleaves deacetylated poly-beta(1,6)-N-acetylglucosamine and can disrupt bacterial biofilms.,Little DJ, Pfoh R, Le Mauff F, Bamford NC, Notte C, Baker P, Guragain M, Robinson H, Pier GB, Nitz M, Deora R, Sheppard DC, Howell PL PLoS Pathog. 2018 Apr 23;14(4):e1006998. doi: 10.1371/journal.ppat.1006998., eCollection 2018 Apr. PMID:29684093<ref>PMID:29684093</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6au1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Alcaligenes bronchisepticus]]
	[[Category: Bamford, N C]]		[[Category: Bamford, N C]]
	[[Category: Howell, P L]]		[[Category: Howell, P L]]

OCA at 05:43, 18 April 2018

OCA — Wed, 18 Apr 2018 05:43:23 GMT

←Older revision		Revision as of 05:43, 18 April 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6au1 is ~~ON HOLD until Paper Publication~~	+	==Structure of the PgaB (BpsB) glycoside hydrolase domain from Bordetella bronchiseptica==
-		+	<StructureSection load='6au1' size='340' side='right' caption='[[6au1]], [[Resolution\|resolution]] 1.76Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6au1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AU1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AU1 FirstGlance]. <br>
-	~~Description~~:	+	</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=6au1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6au1 OCA], [http://pdbe.org/6au1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6au1 RCSB], [http://www.ebi.ac.uk/pdbsum/6au1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6au1 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bamford, N C]]
		+	[[Category: Howell, P L]]
		+	[[Category: Little, D J]]
		+	[[Category: Biofilm]]
		+	[[Category: Deacetylase]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Pnag]]

OCA: Protected "6au1" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 16:47:21 GMT

Protected "6au1" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:47, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 6au1 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 16:47:20 GMT

New page: '''Unreleased structure''' The entry 6au1 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6au1 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]