7t8n - Revision history

OCA at 13:07, 1 March 2024

OCA — Fri, 01 Mar 2024 13:07:44 GMT

←Older revision		Revision as of 13:07, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7t8n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7T8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T8N FirstGlance]. <br>		<table><tr><td colspan='2'>[[7t8n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7T8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T8N FirstGlance]. <br>
-	</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=MG:MAGNESIUM+ION'>MG</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]] 2.85Å</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=MG:MAGNESIUM+ION'>MG</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=7t8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7t8n OCA], [https://pdbe.org/7t8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7t8n RCSB], [https://www.ebi.ac.uk/pdbsum/7t8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7t8n 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=7t8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7t8n OCA], [https://pdbe.org/7t8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7t8n RCSB], [https://www.ebi.ac.uk/pdbsum/7t8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7t8n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PGAA_ECOLI PGAA_ECOLI]] Exports the biofilm adhesin polysaccharide poly-beta-1,6-N-acetyl-D-glucosamine (PGA) across the outer membrane. The PGA transported seems to be partially N-deacetylated since N-deacetylation of PGA by PgaB is needed for PGA export through the PgaA porin. Required for the synthesis of the beta-1,6-GlcNAc polysaccharide (PGA or poly-GlcNAc) that seems to serve as a biofilm adhesin.	+	[https://www.uniprot.org/uniprot/PGAA_ECOLI PGAA_ECOLI] Exports the biofilm adhesin polysaccharide poly-beta-1,6-N-acetyl-D-glucosamine (PGA) across the outer membrane. The PGA transported seems to be partially N-deacetylated since N-deacetylation of PGA by PgaB is needed for PGA export through the PgaA porin. Required for the synthesis of the beta-1,6-GlcNAc polysaccharide (PGA or poly-GlcNAc) that seems to serve as a biofilm adhesin.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The synthesis of exopolysaccharides as biofilm matrix components by pathogens is a crucial factor for chronic infections and antibiotic resistance. Many periplasmic proteins involved in polymer processing and secretion in Gram-negative synthase dependent exopolysaccharide biosynthetic systems have been individually characterized. The operons responsible for the production of PNAG, alginate, cellulose and the Pel polysaccharide each contain a gene that encodes an outer membrane associated tetratricopeptide repeat (TPR) domain containing protein. While the TPR domain has been shown to bind other periplasmic proteins, the functional consequences of these interactions for the polymer remain poorly understood. Herein, we show that the C-terminal TPR region of PgaA interacts with the de-N-acetylase domain of PgaB, and increases its deacetylase activity. Additionally, we found that when the two proteins form a complex, the glycoside hydrolase activity of PgaB is also increased. To better understand structure-function relationships we determined the crystal structure of a stable TPR module, which has a conserved groove formed by three repeat motifs. Tryptophan quenching, mass spectrometry analysis and molecular dynamics simulation studies suggest that the crystallized TPR module can bind PNAG/dPNAG via its electronegative groove on the concave surface, and potentially guide the polymer through the periplasm towards the porin for export. Our results suggest a scaffolding role for the TPR domain that combines PNAG/dPNAG translocation with the modulation of its chemical structure by PgaB.	+
-		+
-	The TPR domain of PgaA is a multifunctional scaffold that binds PNAG and modulates PgaB-dependent polymer processing.,Pfoh R, Subramanian AS, Huang J, Little DJ, Forman A, DiFrancesco BR, Balouchestani-Asli N, Kitova EN, Klassen JS, Pomes R, Nitz M, Howell PL PLoS Pathog. 2022 Aug 5;18(8):e1010750. doi: 10.1371/journal.ppat.1010750., eCollection 2022 Aug. PMID:35930610<ref>PMID:35930610</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 7t8n" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 03:17, 8 September 2022

OCA — Thu, 08 Sep 2022 03:17:26 GMT

←Older revision		Revision as of 03:17, 8 September 2022
Line 3:		Line 3:
	<StructureSection load='7t8n' size='340' side='right'caption='[[7t8n]], [[Resolution\|resolution]] 2.85Å' scene=''>		<StructureSection load='7t8n' size='340' side='right'caption='[[7t8n]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7t8n]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7T8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T8N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7t8n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7T8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T8N FirstGlance]. <br>
	</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=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</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=MG:MAGNESIUM+ION'>MG</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=7t8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7t8n OCA], [https://pdbe.org/7t8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7t8n RCSB], [https://www.ebi.ac.uk/pdbsum/7t8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7t8n 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=7t8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7t8n OCA], [https://pdbe.org/7t8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7t8n RCSB], [https://www.ebi.ac.uk/pdbsum/7t8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7t8n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PGAA_ECOLI PGAA_ECOLI]] Exports the biofilm adhesin polysaccharide poly-beta-1,6-N-acetyl-D-glucosamine (PGA) across the outer membrane. The PGA transported seems to be partially N-deacetylated since N-deacetylation of PGA by PgaB is needed for PGA export through the PgaA porin. Required for the synthesis of the beta-1,6-GlcNAc polysaccharide (PGA or poly-GlcNAc) that seems to serve as a biofilm adhesin.	+	[[https://www.uniprot.org/uniprot/PGAA_ECOLI PGAA_ECOLI]] Exports the biofilm adhesin polysaccharide poly-beta-1,6-N-acetyl-D-glucosamine (PGA) across the outer membrane. The PGA transported seems to be partially N-deacetylated since N-deacetylation of PGA by PgaB is needed for PGA export through the PgaA porin. Required for the synthesis of the beta-1,6-GlcNAc polysaccharide (PGA or poly-GlcNAc) that seems to serve as a biofilm adhesin.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Howell~~, P L~~]]	+	[[Category: Howell PL]]
-	[[Category: Little~~, D J~~]]	+	[[Category: Little DJ]]
-	[[Category: Pfoh, R]]	+	[[Category: Pfoh R]]
-	~~[[Category: Pnag binding module]]~~	+
-	~~[[Category: Pnag secretion]]~~	+
-	~~[[Category: Structural protein~~]]	+

OCA at 06:41, 18 August 2022

OCA — Thu, 18 Aug 2022 06:41:51 GMT

←Older revision		Revision as of 06:41, 18 August 2022
Line 1:		Line 1:

	==Crystal structure of the PNAG binding module PgaA-TPR 220-359==		==Crystal structure of the PNAG binding module PgaA-TPR 220-359==
-	<StructureSection load='7t8n' size='340' side='right'caption='[[7t8n]]' scene=''>	+	<StructureSection load='7t8n' size='340' side='right'caption='[[7t8n]], [[Resolution\|resolution]] 2.85Å' 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=7T8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T8N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7t8n]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7T8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T8N 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=7t8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7t8n OCA], [https://pdbe.org/7t8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7t8n RCSB], [https://www.ebi.ac.uk/pdbsum/7t8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7t8n 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=7t8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7t8n OCA], [https://pdbe.org/7t8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7t8n RCSB], [https://www.ebi.ac.uk/pdbsum/7t8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7t8n ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/PGAA_ECOLI PGAA_ECOLI]] Exports the biofilm adhesin polysaccharide poly-beta-1,6-N-acetyl-D-glucosamine (PGA) across the outer membrane. The PGA transported seems to be partially N-deacetylated since N-deacetylation of PGA by PgaB is needed for PGA export through the PgaA porin. Required for the synthesis of the beta-1,6-GlcNAc polysaccharide (PGA or poly-GlcNAc) that seems to serve as a biofilm adhesin.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The synthesis of exopolysaccharides as biofilm matrix components by pathogens is a crucial factor for chronic infections and antibiotic resistance. Many periplasmic proteins involved in polymer processing and secretion in Gram-negative synthase dependent exopolysaccharide biosynthetic systems have been individually characterized. The operons responsible for the production of PNAG, alginate, cellulose and the Pel polysaccharide each contain a gene that encodes an outer membrane associated tetratricopeptide repeat (TPR) domain containing protein. While the TPR domain has been shown to bind other periplasmic proteins, the functional consequences of these interactions for the polymer remain poorly understood. Herein, we show that the C-terminal TPR region of PgaA interacts with the de-N-acetylase domain of PgaB, and increases its deacetylase activity. Additionally, we found that when the two proteins form a complex, the glycoside hydrolase activity of PgaB is also increased. To better understand structure-function relationships we determined the crystal structure of a stable TPR module, which has a conserved groove formed by three repeat motifs. Tryptophan quenching, mass spectrometry analysis and molecular dynamics simulation studies suggest that the crystallized TPR module can bind PNAG/dPNAG via its electronegative groove on the concave surface, and potentially guide the polymer through the periplasm towards the porin for export. Our results suggest a scaffolding role for the TPR domain that combines PNAG/dPNAG translocation with the modulation of its chemical structure by PgaB.
		+
		+	The TPR domain of PgaA is a multifunctional scaffold that binds PNAG and modulates PgaB-dependent polymer processing.,Pfoh R, Subramanian AS, Huang J, Little DJ, Forman A, DiFrancesco BR, Balouchestani-Asli N, Kitova EN, Klassen JS, Pomes R, Nitz M, Howell PL PLoS Pathog. 2022 Aug 5;18(8):e1010750. doi: 10.1371/journal.ppat.1010750., eCollection 2022 Aug. PMID:35930610<ref>PMID:35930610</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7t8n" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Howell PL]]	+	[[Category: Howell, P L]]
-	[[Category: Little DJ]]	+	[[Category: Little, D J]]
-	[[Category: Pfoh R]]	+	[[Category: Pfoh, R]]
		+	[[Category: Pnag binding module]]
		+	[[Category: Pnag secretion]]
		+	[[Category: Structural protein]]

OCA at 04:53, 3 August 2022

OCA — Wed, 03 Aug 2022 04:53:24 GMT

←Older revision		Revision as of 04:53, 3 August 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7t8n is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of the PNAG binding module PgaA-TPR 220-359==
-		+	<StructureSection load='7t8n' size='340' side='right'caption='[[7t8n]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7T8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T8N 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=7t8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7t8n OCA], [https://pdbe.org/7t8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7t8n RCSB], [https://www.ebi.ac.uk/pdbsum/7t8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7t8n ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Howell PL]]
		+	[[Category: Little DJ]]
		+	[[Category: Pfoh R]]

OCA at 12:03, 29 December 2021

OCA — Wed, 29 Dec 2021 12:03:31 GMT

←Older revision		Revision as of 12:03, 29 December 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7t8n is ON HOLD	+	The entry 7t8n is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7t8n" [edit=sysop:move=sysop]

OCA — Wed, 22 Dec 2021 14:11:12 GMT

Protected "7t8n" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:11, 22 December 2021

OCA: New page: '''Unreleased structure''' The entry 7t8n is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 22 Dec 2021 14:11:10 GMT

New page: '''Unreleased structure''' The entry 7t8n is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7t8n is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]