5u96 - Revision history

OCA at 13:23, 4 October 2023

OCA — Wed, 04 Oct 2023 13:23:30 GMT

←Older revision		Revision as of 13:23, 4 October 2023
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	<StructureSection load='5u96' size='340' side='right'caption='[[5u96]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='5u96' size='340' side='right'caption='[[5u96]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5u96]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"listeria_innocua"_seeliger_and_schoofs_1979 "listeria~~ innocua~~" seeliger and schoofs 1979~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U96 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5U96 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5u96]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Listeria_innocua Listeria innocua]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U96 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5U96 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5uae\|5uae]]</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]] 1.95Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">int ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=1642 "Listeria innocua" Seeliger and Schoofs 1979])~~</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=5u96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u96 OCA], [https://pdbe.org/5u96 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5u96 RCSB], [https://www.ebi.ac.uk/pdbsum/5u96 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5u96 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=5u96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u96 OCA], [~~http~~://pdbe.org/5u96 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5u96 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5u96 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5u96 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q928V6_LISIN Q928V6_LISIN]
	<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: Listeria innocua seeliger and schoofs 1979]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Duyne, G D.Van~~]]	+	[[Category: Listeria innocua]]
-	[[Category: Gupta, K]]	+	[[Category: Gupta K]]
-	[[Category: Sharp, R]]	+	[[Category: Sharp R]]
-	[[Category: ~~Yuan, J B~~]]	+	[[Category: Van Duyne GD]]
-	[[Category: ~~Coiled-coil]]~~	+	[[Category: Yuan JB]]
-	~~[[Category: Recombination]]~~	+
-	~~[[Category: Site-specific recombination~~]]	+

OCA at 09:12, 1 January 2020

OCA — Wed, 01 Jan 2020 09:12:30 GMT

←Older revision		Revision as of 09:12, 1 January 2020
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	==Crystal structure of the coiled-coil domain from Listeria Innocua (Tetragonal Form)==		==Crystal structure of the coiled-coil domain from Listeria Innocua (Tetragonal Form)==
-	<StructureSection load='5u96' size='340' side='right' caption='[[5u96]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='5u96' size='340' side='right'caption='[[5u96]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5u96]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"listeria_innocua"_seeliger_and_schoofs_1979 "listeria innocua" seeliger and schoofs 1979]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U96 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U96 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5u96]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"listeria_innocua"_seeliger_and_schoofs_1979 "listeria innocua" seeliger and schoofs 1979]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U96 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U96 FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Listeria innocua seeliger and schoofs 1979]]		[[Category: Listeria innocua seeliger and schoofs 1979]]
		+	[[Category: Large Structures]]
	[[Category: Duyne, G D.Van]]		[[Category: Duyne, G D.Van]]
	[[Category: Gupta, K]]		[[Category: Gupta, K]]

OCA at 08:43, 19 December 2018

OCA — Wed, 19 Dec 2018 08:43:12 GMT

←Older revision		Revision as of 08:43, 19 December 2018
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	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	Serine integrases ~~catalyze the integration of~~ bacteriophage ~~DNA into a host genome by~~ site-specific ~~recombination between 'attachment sites' in the phage (attP)~~ and ~~the host (attB)~~. The reaction is highly directional; ~~the reverse excision reaction~~ between the ~~product attL and attR sites does not occur in the absence of a~~ phage~~-encoded factor, nor does recombination occur between other pairings of~~ attachment ~~sites. A mechanistic understanding of how these enzymes achieve~~ site~~-selectivity~~ and ~~directionality has been limited by a lack of structural models. Here, we report~~ the ~~structure of the C-terminal domains of a serine integrase bound to an attP DNA half-~~site~~. The structure leads directly~~ to ~~models for understanding how~~ the ~~integrase-bound attP and attB~~ sites ~~differ, why these enzymes preferentially form attP x attB synaptic complexes to initiate recombination,~~ and ~~how attL x~~ attR ~~recombination~~ is ~~prevented~~. In ~~these models~~, ~~different domain organizations on attP vs. attB half~~-~~sites allow attachment-site specific interactions to form between~~ integrase subunits ~~via an unusual protruding coiled-coil motif. These interactions~~ are ~~used~~ to ~~preferentially synapse~~ integrase-bound ~~attP~~ and ~~attB~~ and ~~inhibit synapsis~~ of ~~integrase-bound~~ attL and attR. ~~The results~~ provide a ~~structural framework~~ for understanding~~, testing and engineering~~ serine integrase ~~function~~.	+	Serine integrases are bacteriophage enzymes that carry out site-specific integration and excision of their viral genomes. The integration reaction is highly directional; recombination between the phage attachment site attP and the host attachment site attB to form the hybrid sites attL and attR is essentially irreversible. In a recent model, extended coiled-coil (CC) domains in the integrase subunits are proposed to interact in a way that favors the attPxattB reaction but inhibits the attLxattR reaction. Here, we show for the Listeria innocua integrase (LI Int) system that the CC domain promotes self-interaction in isolated Int and when Int is bound to attachment sites. Three independent crystal structures of the CC domain reveal the molecular nature of the CC dimer interface. Alanine substitutions of key residues in the interface support the functional significance of the structural model and indicate that the same interaction is responsible for promoting integration and for inhibiting excision. An updated model of a LI IntattL complex that incorporates the high resolution CC dimer structure provides insights that help to explain the unusual CC dimer structure and potential sources of stability in IntattL and Int*attR complexes. Together, the data provide a molecular basis for understanding serine integrase directionality.

-	~~Attachment site recognition and regulation of directionality by the~~ serine ~~integrases~~.,~~Rutherford~~ K, Yuan P, ~~Perry K, Sharp R~~, Van Duyne GD Nucleic Acids Res. ~~2013 Sep 1~~;41(17):~~8341~~-56. doi: 10.1093/nar/~~gkt580. Epub 2013 , Jul 2~~. PMID:~~23821671~~<ref>PMID:~~23821671~~</ref>	+	Coiled-coil interactions mediate serine integrase directionality.,Gupta K, Sharp R, Yuan JB, Li H, Van Duyne GD Nucleic Acids Res. 2017 Jul 7;45(12):7339-7353. doi: 10.1093/nar/gkx474. PMID:28549184<ref>PMID:28549184</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

OCA at 14:31, 6 November 2017

OCA — Mon, 06 Nov 2017 14:31:52 GMT

←Older revision		Revision as of 14:31, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5u96' size='340' side='right' caption='[[5u96]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='5u96' size='340' side='right' caption='[[5u96]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5u96]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U96 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U96 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5u96]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"listeria_innocua"_seeliger_and_schoofs_1979 "listeria innocua" seeliger and schoofs 1979]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U96 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U96 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uae\|5uae]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uae\|5uae]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">int ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1642 "Listeria innocua" Seeliger and Schoofs 1979])</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=5u96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u96 OCA], [http://pdbe.org/5u96 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u96 RCSB], [http://www.ebi.ac.uk/pdbsum/5u96 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u96 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=5u96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u96 OCA], [http://pdbe.org/5u96 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u96 RCSB], [http://www.ebi.ac.uk/pdbsum/5u96 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u96 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Listeria innocua seeliger and schoofs 1979]]
	[[Category: Duyne, G D.Van]]		[[Category: Duyne, G D.Van]]
	[[Category: Gupta, K]]		[[Category: Gupta, K]]

OCA at 13:37, 24 May 2017

OCA — Wed, 24 May 2017 13:37:33 GMT

←Older revision		Revision as of 13:37, 24 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5u96 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of the coiled-coil domain from Listeria Innocua (Tetragonal Form)==
		+	<StructureSection load='5u96' size='340' side='right' caption='[[5u96]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5u96]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U96 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U96 FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uae\|5uae]]</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=5u96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u96 OCA], [http://pdbe.org/5u96 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u96 RCSB], [http://www.ebi.ac.uk/pdbsum/5u96 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u96 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Serine integrases catalyze the integration of bacteriophage DNA into a host genome by site-specific recombination between 'attachment sites' in the phage (attP) and the host (attB). The reaction is highly directional; the reverse excision reaction between the product attL and attR sites does not occur in the absence of a phage-encoded factor, nor does recombination occur between other pairings of attachment sites. A mechanistic understanding of how these enzymes achieve site-selectivity and directionality has been limited by a lack of structural models. Here, we report the structure of the C-terminal domains of a serine integrase bound to an attP DNA half-site. The structure leads directly to models for understanding how the integrase-bound attP and attB sites differ, why these enzymes preferentially form attP x attB synaptic complexes to initiate recombination, and how attL x attR recombination is prevented. In these models, different domain organizations on attP vs. attB half-sites allow attachment-site specific interactions to form between integrase subunits via an unusual protruding coiled-coil motif. These interactions are used to preferentially synapse integrase-bound attP and attB and inhibit synapsis of integrase-bound attL and attR. The results provide a structural framework for understanding, testing and engineering serine integrase function.

-	~~Authors: Gupta~~, K., ~~Van Duyne~~, ~~G.D.~~, Sharp, R., ~~Yuan, J~~.B.	+	Attachment site recognition and regulation of directionality by the serine integrases.,Rutherford K, Yuan P, Perry K, Sharp R, Van Duyne GD Nucleic Acids Res. 2013 Sep 1;41(17):8341-56. doi: 10.1093/nar/gkt580. Epub 2013 , Jul 2. PMID:23821671<ref>PMID:23821671</ref>

-	~~Description: Crystal structure~~ of the ~~coiled~~-~~coil domain from Listeria Innocua (Tetragonal Form)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5u96" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Duyne, G D.Van]]
	[[Category: Gupta, K]]		[[Category: Gupta, K]]
	[[Category: Sharp, R]]		[[Category: Sharp, R]]
-	[[Category: Yuan, J.B]]	+	[[Category: Yuan, J B]]
-	[[Category: ~~Van Duyne, G.D~~]]	+	[[Category: Coiled-coil]]
		+	[[Category: Recombination]]
		+	[[Category: Site-specific recombination]]

OCA at 10:57, 5 April 2017

OCA — Wed, 05 Apr 2017 10:57:41 GMT

←Older revision		Revision as of 10:57, 5 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5u96 is ON HOLD	+	The entry 5u96 is ON HOLD until Paper Publication

	Authors: Gupta, K., Van Duyne, G.D., Sharp, R., Yuan, J.B.		Authors: Gupta, K., Van Duyne, G.D., Sharp, R., Yuan, J.B.

OCA at 18:51, 15 March 2017

OCA — Wed, 15 Mar 2017 18:51:35 GMT

←Older revision		Revision as of 18:51, 15 March 2017
Line 7:		Line 7:
	Description: Crystal structure of the coiled-coil domain from Listeria Innocua (Tetragonal Form)		Description: Crystal structure of the coiled-coil domain from Listeria Innocua (Tetragonal Form)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Gupta, K]]
	[[Category: Sharp, R]]		[[Category: Sharp, R]]
	[[Category: Yuan, J.B]]		[[Category: Yuan, J.B]]
	[[Category: Van Duyne, G.D]]		[[Category: Van Duyne, G.D]]
-	[[Category: Gupta, K]]

OCA at 14:16, 9 March 2017

OCA — Thu, 09 Mar 2017 14:16:41 GMT

←Older revision		Revision as of 14:16, 9 March 2017
Line 3:		Line 3:
	The entry 5u96 is ON HOLD		The entry 5u96 is ON HOLD

-	Authors: Gupta, K., Van Duyne, G.D.	+	Authors: Gupta, K., Van Duyne, G.D., Sharp, R., Yuan, J.B.

	Description: Crystal structure of the coiled-coil domain from Listeria Innocua (Tetragonal Form)		Description: Crystal structure of the coiled-coil domain from Listeria Innocua (Tetragonal Form)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Sharp, R]]
		+	[[Category: Yuan, J.B]]
	[[Category: Van Duyne, G.D]]		[[Category: Van Duyne, G.D]]
	[[Category: Gupta, K]]		[[Category: Gupta, K]]

OCA: Protected "5u96" [edit=sysop:move=sysop]

OCA — Thu, 22 Dec 2016 20:34:28 GMT

Protected "5u96" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:34, 22 December 2016

OCA: New page: '''Unreleased structure''' The entry 5u96 is ON HOLD Authors: Gupta, K., Van Duyne, G.D. Description: Crystal structure of the coiled-coil domain from Listeria Innocua (Tetragonal Form...

OCA — Thu, 22 Dec 2016 20:34:26 GMT

New page: '''Unreleased structure''' The entry 5u96 is ON HOLD Authors: Gupta, K., Van Duyne, G.D. Description: Crystal structure of the coiled-coil domain from Listeria Innocua (Tetragonal Form...

New page

'''Unreleased structure'''

The entry 5u96 is ON HOLD

Authors: Gupta, K., Van Duyne, G.D.

Description: Crystal structure of the coiled-coil domain from Listeria Innocua (Tetragonal Form)
[[Category: Unreleased Structures]]
[[Category: Van Duyne, G.D]]
[[Category: Gupta, K]]