5tu7 - Revision history

OCA at 14:23, 6 March 2024

OCA — Wed, 06 Mar 2024 14:23:18 GMT

←Older revision		Revision as of 14:23, 6 March 2024
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	<StructureSection load='5tu7' size='340' side='right'caption='[[5tu7]], [[Resolution\|resolution]] 3.34Å' scene=''>		<StructureSection load='5tu7' size='340' side='right'caption='[[5tu7]], [[Resolution\|resolution]] 3.34Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tu7]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Staeq Staeq~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TU7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TU7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tu7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_epidermidis_RP62A Staphylococcus epidermidis RP62A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TU7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TU7 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5tu8\|5tu8]], [[5tu9\|5tu9]]</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]] 3.34Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">aap, SERP2398 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=176279 STAEQ])~~</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=5tu7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tu7 OCA], [https://pdbe.org/5tu7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tu7 RCSB], [https://www.ebi.ac.uk/pdbsum/5tu7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tu7 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=5tu7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tu7 OCA], [~~http~~://pdbe.org/5tu7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5tu7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5tu7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5tu7 ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q5HKE8_STAEQ Q5HKE8_STAEQ]
-	Staphylococcus epidermidis is an opportunistic pathogen that can form robust biofilms that render the bacteria resistant to antibiotic action and immune responses. Intercellular adhesion in S. epidermidis biofilms is mediated by the cell wall-associated Accumulation-Associated Protein (Aap), via zinc-mediated self-assembly of its B-repeat region. This region contains up to 17 nearly-identical sequence repeats, with each repeat assumed to be functionally equivalent. However, Aap B-repeats exist as two subtypes, defined by a cluster of consensus or variant amino acids. These variable residues are positioned near the zinc-binding (and dimerization) site and the stability determinant for the B-repeat fold. We have characterized four B-repeat constructs to assess the functional relevance of the two Aap B-repeat subtypes. Analytical ultracentrifugation experiments demonstrated that constructs with the variant sequence show reduced or absent Zn2+-induced dimerization. Likewise, circular dichroism thermal denaturation experiments showed that the variant sequence could significantly stabilize the fold, depending on its location within the construct. Crystal structures of three of the constructs revealed that the side chains from the variant sequence form an extensive bonding network that can stabilize the fold. Furthermore, altered distribution of charged residues between consensus and variant sequences changes the electrostatic potential in the vicinity of the Zn2+ binding site, providing a mechanistic explanation for the loss of zinc-induced dimerization in the variant constructs. These data suggest an assembly code that defines preferred oligomerization modes of the B-repeat region of Aap and a slip-grip model for initial contact and firm intercellular adhesion during biofilm formation.	+
-		+
-	~~Functional consequences of B-repeat sequence variation in the Staphylococcal biofilm protein Aap~~: ~~Deciphering the assembly code.,Shelton CL, Conrady DG, Herr AB Biochem J. 2016 Nov 21. pii: BCJ20160675. PMID:27872164<ref>PMID:27872164<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5tu7" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Staeq~~]]	+	[[Category: Staphylococcus epidermidis RP62A]]
-	[[Category: Conrady~~, D G~~]]	+	[[Category: Conrady DG]]
-	[[Category: Herr~~, A B~~]]	+	[[Category: Herr AB]]
-	[[Category: Shelton~~, C L]]~~	+	[[Category: Shelton CL]]
-	~~[[Category: Biofilm intercellular adhesion staphylococcus aap]]~~	+
-	~~[[Category: Protein binding~~]]	+

OCA at 12:27, 17 July 2019

OCA — Wed, 17 Jul 2019 12:27:22 GMT

←Older revision		Revision as of 12:27, 17 July 2019
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	==Crystal structure of Staphylococcus epidermidis Aap G511-spacer-G513 (consensus G5-spacer-consensus G5)==		==Crystal structure of Staphylococcus epidermidis Aap G511-spacer-G513 (consensus G5-spacer-consensus G5)==
-	<StructureSection load='5tu7' size='340' side='right' caption='[[5tu7]], [[Resolution\|resolution]] 3.34Å' scene=''>	+	<StructureSection load='5tu7' size='340' side='right'caption='[[5tu7]], [[Resolution\|resolution]] 3.34Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5tu7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Staeq Staeq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TU7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TU7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5tu7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Staeq Staeq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TU7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TU7 FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Staeq]]		[[Category: Staeq]]
	[[Category: Conrady, D G]]		[[Category: Conrady, D G]]

OCA at 19:19, 15 November 2017

OCA — Wed, 15 Nov 2017 19:19:19 GMT

←Older revision		Revision as of 19:19, 15 November 2017
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	<StructureSection load='5tu7' size='340' side='right' caption='[[5tu7]], [[Resolution\|resolution]] 3.34Å' scene=''>		<StructureSection load='5tu7' size='340' side='right' caption='[[5tu7]], [[Resolution\|resolution]] 3.34Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tu7]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TU7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TU7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tu7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Staeq Staeq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TU7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TU7 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tu8\|5tu8]], [[5tu9\|5tu9]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tu8\|5tu8]], [[5tu9\|5tu9]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aap, SERP2398 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176279 STAEQ])</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=5tu7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tu7 OCA], [http://pdbe.org/5tu7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tu7 RCSB], [http://www.ebi.ac.uk/pdbsum/5tu7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tu7 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=5tu7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tu7 OCA], [http://pdbe.org/5tu7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tu7 RCSB], [http://www.ebi.ac.uk/pdbsum/5tu7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tu7 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Staeq]]
	[[Category: Conrady, D G]]		[[Category: Conrady, D G]]
	[[Category: Herr, A B]]		[[Category: Herr, A B]]

OCA at 21:30, 22 December 2016

OCA — Thu, 22 Dec 2016 21:30:22 GMT

←Older revision		Revision as of 21:30, 22 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5tu7 is ~~ON HOLD~~	+	==Crystal structure of Staphylococcus epidermidis Aap G511-spacer-G513 (consensus G5-spacer-consensus G5)==
		+	<StructureSection load='5tu7' size='340' side='right' caption='[[5tu7]], [[Resolution\|resolution]] 3.34Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5tu7]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TU7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TU7 FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tu8\|5tu8]], [[5tu9\|5tu9]]</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=5tu7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tu7 OCA], [http://pdbe.org/5tu7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tu7 RCSB], [http://www.ebi.ac.uk/pdbsum/5tu7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tu7 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Staphylococcus epidermidis is an opportunistic pathogen that can form robust biofilms that render the bacteria resistant to antibiotic action and immune responses. Intercellular adhesion in S. epidermidis biofilms is mediated by the cell wall-associated Accumulation-Associated Protein (Aap), via zinc-mediated self-assembly of its B-repeat region. This region contains up to 17 nearly-identical sequence repeats, with each repeat assumed to be functionally equivalent. However, Aap B-repeats exist as two subtypes, defined by a cluster of consensus or variant amino acids. These variable residues are positioned near the zinc-binding (and dimerization) site and the stability determinant for the B-repeat fold. We have characterized four B-repeat constructs to assess the functional relevance of the two Aap B-repeat subtypes. Analytical ultracentrifugation experiments demonstrated that constructs with the variant sequence show reduced or absent Zn2+-induced dimerization. Likewise, circular dichroism thermal denaturation experiments showed that the variant sequence could significantly stabilize the fold, depending on its location within the construct. Crystal structures of three of the constructs revealed that the side chains from the variant sequence form an extensive bonding network that can stabilize the fold. Furthermore, altered distribution of charged residues between consensus and variant sequences changes the electrostatic potential in the vicinity of the Zn2+ binding site, providing a mechanistic explanation for the loss of zinc-induced dimerization in the variant constructs. These data suggest an assembly code that defines preferred oligomerization modes of the B-repeat region of Aap and a slip-grip model for initial contact and firm intercellular adhesion during biofilm formation.

-	~~Authors~~:	+	Functional consequences of B-repeat sequence variation in the Staphylococcal biofilm protein Aap: Deciphering the assembly code.,Shelton CL, Conrady DG, Herr AB Biochem J. 2016 Nov 21. pii: BCJ20160675. PMID:27872164<ref>PMID:27872164</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5tu7" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Conrady, D G]]
		+	[[Category: Herr, A B]]
		+	[[Category: Shelton, C L]]
		+	[[Category: Biofilm intercellular adhesion staphylococcus aap]]
		+	[[Category: Protein binding]]

OCA at 17:20, 15 December 2016

OCA — Thu, 15 Dec 2016 17:20:31 GMT

←Older revision		Revision as of 17:20, 15 December 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5tu7 is ON HOLD ~~until sometime in the future~~	+	The entry 5tu7 is ON HOLD

	Authors:		Authors:

OCA: Protected "5tu7" [edit=sysop:move=sysop]

OCA — Fri, 09 Dec 2016 17:52:50 GMT

Protected "5tu7" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:52, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5tu7 is ON HOLD until sometime in the future Authors: Description: Category: Unreleased Structures

OCA — Fri, 09 Dec 2016 17:52:49 GMT

New page: '''Unreleased structure''' The entry 5tu7 is ON HOLD until sometime in the future Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5tu7 is ON HOLD until sometime in the future

Authors:

Description:
[[Category: Unreleased Structures]]