6p0u - Revision history

OCA at 07:20, 11 October 2023

2023-10-11T07:20:54Z

←Older revision		Revision as of 07:20, 11 October 2023
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	<StructureSection load='6p0u' size='340' side='right'caption='[[6p0u]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='6p0u' size='340' side='right'caption='[[6p0u]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6p0u]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacteriophage_lambda Bacteriophage lambda~~] and [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P0U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6P0U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6p0u]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli], [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Escherichia_virus_Lambda Escherichia virus Lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P0U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6P0U FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~fis~~, ~~b3261, JW3229 (~~[~~http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI~~]~~), xis ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=10710 Bacteriophage lambda])~~</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]] 3.3Å</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=6p0u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p0u OCA], [~~http~~://pdbe.org/6p0u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6p0u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6p0u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6p0u 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=6p0u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p0u OCA], [https://pdbe.org/6p0u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6p0u RCSB], [https://www.ebi.ac.uk/pdbsum/6p0u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6p0u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http://www.uniprot.org/uniprot/VXIS_LAMBD VXIS_LAMBD]] Excisionase and integrase are necessary for the excision of prophage from the host genome by site-specific recombination at the att site. [[http~~://www.uniprot.org/uniprot/FIS_ECOLI FIS_ECOLI]] Activates ribosomal RNA transcription, as well other genes. Plays a direct role in upstream activation of rRNA promoters. Binds to a recombinational enhancer sequence that is required to stimulate hin-mediated DNA inversion. Prevents initiation of DNA replication from oriC.<ref>PMID:2209559</ref> <ref>PMID:8836178</ref>	+	[https://www.uniprot.org/uniprot/FIS_ECOLI FIS_ECOLI] Activates ribosomal RNA transcription, as well other genes. Plays a direct role in upstream activation of rRNA promoters. Binds to a recombinational enhancer sequence that is required to stimulate hin-mediated DNA inversion. Prevents initiation of DNA replication from oriC.<ref>PMID:2209559</ref> <ref>PMID:8836178</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacteriophage lambda~~]]	+	[[Category: Escherichia coli]]
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
		+	[[Category: Escherichia virus Lambda]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cascio, D]]	+	[[Category: Cascio D]]
-	[[Category: Hancock~~, S P~~]]	+	[[Category: Hancock SP]]
-	[[Category: Johnson~~, R C]]~~	+	[[Category: Johnson RC]]
-	~~[[Category: Cooperative binding]]~~	+
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Dna binding protein-dna complex]]~~	+
-	~~[[Category: Dna shape]]~~	+
-	~~[[Category: Protein-dna ternary complex~~]]	+

OCA at 09:33, 8 January 2020

2020-01-08T09:33:56Z

←Older revision		Revision as of 09:33, 8 January 2020
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/VXIS_LAMBD VXIS_LAMBD]] Excisionase and integrase are necessary for the excision of prophage from the host genome by site-specific recombination at the att site. [[http://www.uniprot.org/uniprot/FIS_ECOLI FIS_ECOLI]] Activates ribosomal RNA transcription, as well other genes. Plays a direct role in upstream activation of rRNA promoters. Binds to a recombinational enhancer sequence that is required to stimulate hin-mediated DNA inversion. Prevents initiation of DNA replication from oriC.<ref>PMID:2209559</ref> <ref>PMID:8836178</ref>		[[http://www.uniprot.org/uniprot/VXIS_LAMBD VXIS_LAMBD]] Excisionase and integrase are necessary for the excision of prophage from the host genome by site-specific recombination at the att site. [[http://www.uniprot.org/uniprot/FIS_ECOLI FIS_ECOLI]] Activates ribosomal RNA transcription, as well other genes. Plays a direct role in upstream activation of rRNA promoters. Binds to a recombinational enhancer sequence that is required to stimulate hin-mediated DNA inversion. Prevents initiation of DNA replication from oriC.<ref>PMID:2209559</ref> <ref>PMID:8836178</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Localized arrays of proteins cooperatively assemble onto chromosomes to control DNA activity in many contexts. Binding cooperativity is often mediated by specific protein-protein interactions, but cooperativity through DNA structure is becoming increasingly recognized as an additional mechanism. During the site-specific DNA recombination reaction that excises phage lambda from the chromosome, the bacterial DNA architectural protein Fis recruits multiple lambda-encoded Xis proteins to the attR recombination site. Here, we report X-ray crystal structures of DNA complexes containing Fis + Xis, which show little, if any, contacts between the two proteins. Comparisons with structures of DNA complexes containing only Fis or Xis, together with mutant protein and DNA binding studies, support a mechanism for cooperative protein binding solely by DNA allostery. Fis binding both molds the minor groove to potentiate insertion of the Xis beta-hairpin wing motif and bends the DNA to facilitate Xis-DNA contacts within the major groove. The Fis-structured minor groove shape that is optimized for Xis binding requires a precisely positioned pyrimidine-purine base-pair step, whose location has been shown to modulate minor groove widths in Fis-bound complexes to different DNA targets.
		+
		+	Cooperative DNA binding by proteins through DNA shape complementarity.,Hancock SP, Cascio D, Johnson RC Nucleic Acids Res. 2019 Sep 19;47(16):8874-8887. doi: 10.1093/nar/gkz642. PMID:31616952<ref>PMID:31616952</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6p0u" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 12:02, 1 January 2020

2020-01-01T12:02:01Z

←Older revision		Revision as of 12:02, 1 January 2020
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	<StructureSection load='6p0u' size='340' side='right'caption='[[6p0u]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='6p0u' size='340' side='right'caption='[[6p0u]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6p0u]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P0U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P0U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6p0u]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_lambda Bacteriophage lambda] and [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P0U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P0U FirstGlance]. <br>
-	</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=6p0u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p0u OCA], [http://pdbe.org/6p0u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p0u RCSB], [http://www.ebi.ac.uk/pdbsum/6p0u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p0u ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fis, b3261, JW3229 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), xis ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10710 Bacteriophage lambda])</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=6p0u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p0u OCA], [http://pdbe.org/6p0u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p0u RCSB], [http://www.ebi.ac.uk/pdbsum/6p0u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p0u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/VXIS_LAMBD VXIS_LAMBD]] Excisionase and integrase are necessary for the excision of prophage from the host genome by site-specific recombination at the att site. [[http://www.uniprot.org/uniprot/FIS_ECOLI FIS_ECOLI]] Activates ribosomal RNA transcription, as well other genes. Plays a direct role in upstream activation of rRNA promoters. Binds to a recombinational enhancer sequence that is required to stimulate hin-mediated DNA inversion. Prevents initiation of DNA replication from oriC.<ref>PMID:2209559</ref> <ref>PMID:8836178</ref>		[[http://www.uniprot.org/uniprot/VXIS_LAMBD VXIS_LAMBD]] Excisionase and integrase are necessary for the excision of prophage from the host genome by site-specific recombination at the att site. [[http://www.uniprot.org/uniprot/FIS_ECOLI FIS_ECOLI]] Activates ribosomal RNA transcription, as well other genes. Plays a direct role in upstream activation of rRNA promoters. Binds to a recombinational enhancer sequence that is required to stimulate hin-mediated DNA inversion. Prevents initiation of DNA replication from oriC.<ref>PMID:2209559</ref> <ref>PMID:8836178</ref>
		+
		+	==See Also==
		+	*[[FIS protein\|FIS protein]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacteriophage lambda]]
		+	[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Cascio, D]]		[[Category: Cascio, D]]

OCA at 06:13, 19 June 2019

2019-06-19T06:13:48Z

←Older revision		Revision as of 06:13, 19 June 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6p0u ~~is ON HOLD~~	+	==Crystal structure of ternary DNA complex " FX(1-2)-2Xis" containing E. coli Fis and phage lambda Xis==
-		+	<StructureSection load='6p0u' size='340' side='right'caption='[[6p0u]], [[Resolution\|resolution]] 3.30Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6p0u]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P0U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P0U FirstGlance]. <br>
-	~~Description~~:	+	</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=6p0u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p0u OCA], [http://pdbe.org/6p0u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p0u RCSB], [http://www.ebi.ac.uk/pdbsum/6p0u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p0u ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VXIS_LAMBD VXIS_LAMBD]] Excisionase and integrase are necessary for the excision of prophage from the host genome by site-specific recombination at the att site. [[http://www.uniprot.org/uniprot/FIS_ECOLI FIS_ECOLI]] Activates ribosomal RNA transcription, as well other genes. Plays a direct role in upstream activation of rRNA promoters. Binds to a recombinational enhancer sequence that is required to stimulate hin-mediated DNA inversion. Prevents initiation of DNA replication from oriC.<ref>PMID:2209559</ref> <ref>PMID:8836178</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Cascio, D]]
		+	[[Category: Hancock, S P]]
		+	[[Category: Johnson, R C]]
		+	[[Category: Cooperative binding]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Dna shape]]
		+	[[Category: Protein-dna ternary complex]]

OCA: Protected "6p0u" [edit=sysop:move=sysop]

2019-05-29T04:33:52Z

Protected "6p0u" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:33, 29 May 2019

OCA: New page: '''Unreleased structure''' The entry 6p0u is ON HOLD Authors: Description: Category: Unreleased Structures

2019-05-29T04:33:50Z

New page: '''Unreleased structure''' The entry 6p0u is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6p0u is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]