2l93 - Revision history

OCA at 06:54, 1 May 2024

OCA — Wed, 01 May 2024 06:54:33 GMT

←Older revision		Revision as of 06:54, 1 May 2024
Line 9:		Line 9:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/HNS_SALTY HNS_SALTY] H-NS binds tightly to ds-DNA, increases its thermal stability and inhibits transcription. It also binds to ss-DNA and RNA but with a much lower affinity. H-NS has possible histone-like function. May be a global transcriptional regulator through its ability to bind to curved DNA sequences, which are found in regions upstream of a certain subset of promoters. It plays a role in the thermal control of pili production. It is subject to transcriptional auto-repression. It binds preferentially to the upstream region of its own gene recognizing two segments of DNA on both sides of a bend centered around -150 (By similarity).		[https://www.uniprot.org/uniprot/HNS_SALTY HNS_SALTY] H-NS binds tightly to ds-DNA, increases its thermal stability and inhibits transcription. It also binds to ss-DNA and RNA but with a much lower affinity. H-NS has possible histone-like function. May be a global transcriptional regulator through its ability to bind to curved DNA sequences, which are found in regions upstream of a certain subset of promoters. It plays a role in the thermal control of pili production. It is subject to transcriptional auto-repression. It binds preferentially to the upstream region of its own gene recognizing two segments of DNA on both sides of a bend centered around -150 (By similarity).
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	H-NS and Lsr2 are nucleoid-associated proteins from Gram-negative bacteria and Mycobacteria, respectively, that play an important role in the silencing of horizontally acquired foreign DNA that is more AT-rich than the resident genome. Despite the fact that Lsr2 and H-NS proteins are dissimilar in sequence and structure, they serve apparently similar functions and can functionally complement one another. The mechanism by which these xenogeneic silencers selectively target AT-rich DNA has been enigmatic. We performed high-resolution protein binding microarray analysis to simultaneously assess the binding preference of H-NS and Lsr2 for all possible 8-base sequences. Concurrently, we performed a detailed structure-function relationship analysis of their C-terminal DNA binding domains by NMR. Unexpectedly, we found that H-NS and Lsr2 use a common DNA binding mechanism where a short loop containing a "Q/RGR" motif selectively interacts with the DNA minor groove, where the highest affinity is for AT-rich sequences that lack A-tracts. Mutations of the Q/RGR motif abolished DNA binding activity. Netropsin, a DNA minor groove-binding molecule effectively outcompeted H-NS and Lsr2 for binding to AT-rich sequences. These results provide a unified molecular mechanism to explain findings related to xenogeneic silencing proteins, including their lack of apparent sequence specificity but preference for AT-rich sequences. Our findings also suggest that structural information contained within the DNA minor groove is deciphered by xenogeneic silencing proteins to distinguish genetic material that is self from nonself.
-
-	Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins.,Gordon BR, Li Y, Cote A, Weirauch MT, Ding P, Hughes TR, Navarre WW, Xia B, Liu J Proc Natl Acad Sci U S A. 2011 Jun 28;108(26):10690-5. Epub 2011 Jun 14. PMID:21673140<ref>PMID:21673140</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2l93" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 12:13, 15 November 2023

OCA — Wed, 15 Nov 2023 12:13:46 GMT

←Older revision		Revision as of 12:13, 15 November 2023
Line 1:		Line 1:

	==Solution structure of the C-terminal domain of Salmonella H-NS==		==Solution structure of the C-terminal domain of Salmonella H-NS==
-	<StructureSection load='2l93' size='340' side='right'caption='[[2l93~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='2l93' size='340' side='right'caption='[[2l93]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2l93]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L93 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2L93 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2l93]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L93 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2L93 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'>[[2l92\|2l92]]</div~~></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2l93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l93 OCA], [https://pdbe.org/2l93 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2l93 RCSB], [https://www.ebi.ac.uk/pdbsum/2l93 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2l93 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=2l93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l93 OCA], [https://pdbe.org/2l93 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2l93 RCSB], [https://www.ebi.ac.uk/pdbsum/2l93 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2l93 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/HNS_SALTY HNS_SALTY]] H-NS binds tightly to ds-DNA, increases its thermal stability and inhibits transcription. It also binds to ss-DNA and RNA but with a much lower affinity. H-NS has possible histone-like function. May be a global transcriptional regulator through its ability to bind to curved DNA sequences, which are found in regions upstream of a certain subset of promoters. It plays a role in the thermal control of pili production. It is subject to transcriptional auto-repression. It binds preferentially to the upstream region of its own gene recognizing two segments of DNA on both sides of a bend centered around -150 (By similarity).	+	[https://www.uniprot.org/uniprot/HNS_SALTY HNS_SALTY] H-NS binds tightly to ds-DNA, increases its thermal stability and inhibits transcription. It also binds to ss-DNA and RNA but with a much lower affinity. H-NS has possible histone-like function. May be a global transcriptional regulator through its ability to bind to curved DNA sequences, which are found in regions upstream of a certain subset of promoters. It plays a role in the thermal control of pili production. It is subject to transcriptional auto-repression. It binds preferentially to the upstream region of its own gene recognizing two segments of DNA on both sides of a bend centered around -150 (By similarity).
	<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: Bacillus typhimurium loeffler 1892]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Li, Y~~]]	+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
-	[[Category: ~~At hook]]~~	+	[[Category: Li Y]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: H-n~~]]	+

OCA at 07:49, 9 February 2022

OCA — Wed, 09 Feb 2022 07:49:38 GMT

←Older revision		Revision as of 07:49, 9 February 2022
Line 3:		Line 3:
	<StructureSection load='2l93' size='340' side='right'caption='[[2l93]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2l93' size='340' side='right'caption='[[2l93]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2l93]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L93 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2L93 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2l93]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L93 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2L93 FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2l92\|2l92]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2l92\|2l92]]</div></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=2l93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l93 OCA], [~~http~~://pdbe.org/2l93 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2l93 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2l93 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2l93 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=2l93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l93 OCA], [https://pdbe.org/2l93 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2l93 RCSB], [https://www.ebi.ac.uk/pdbsum/2l93 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2l93 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/HNS_SALTY HNS_SALTY]] H-NS binds tightly to ds-DNA, increases its thermal stability and inhibits transcription. It also binds to ss-DNA and RNA but with a much lower affinity. H-NS has possible histone-like function. May be a global transcriptional regulator through its ability to bind to curved DNA sequences, which are found in regions upstream of a certain subset of promoters. It plays a role in the thermal control of pili production. It is subject to transcriptional auto-repression. It binds preferentially to the upstream region of its own gene recognizing two segments of DNA on both sides of a bend centered around -150 (By similarity).	+	[[https://www.uniprot.org/uniprot/HNS_SALTY HNS_SALTY]] H-NS binds tightly to ds-DNA, increases its thermal stability and inhibits transcription. It also binds to ss-DNA and RNA but with a much lower affinity. H-NS has possible histone-like function. May be a global transcriptional regulator through its ability to bind to curved DNA sequences, which are found in regions upstream of a certain subset of promoters. It plays a role in the thermal control of pili production. It is subject to transcriptional auto-repression. It binds preferentially to the upstream region of its own gene recognizing two segments of DNA on both sides of a bend centered around -150 (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 07:00, 6 May 2020

OCA — Wed, 06 May 2020 07:00:51 GMT

←Older revision		Revision as of 07:00, 6 May 2020
Line 1:		Line 1:

	==Solution structure of the C-terminal domain of Salmonella H-NS==		==Solution structure of the C-terminal domain of Salmonella H-NS==
-	<StructureSection load='2l93' size='340' side='right' caption='[[2l93]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='2l93' size='340' side='right'caption='[[2l93]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2l93]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L93 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2L93 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2l93]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L93 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2L93 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2l92\|2l92]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2l92\|2l92]]</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=2l93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l93 OCA], [http://pdbe.org/2l93 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2l93 RCSB], [http://www.ebi.ac.uk/pdbsum/2l93 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2l93 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2l93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l93 OCA], [http://pdbe.org/2l93 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2l93 RCSB], [http://www.ebi.ac.uk/pdbsum/2l93 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2l93 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus typhimurium loeffler 1892]]		[[Category: Bacillus typhimurium loeffler 1892]]
		+	[[Category: Large Structures]]
	[[Category: Li, Y]]		[[Category: Li, Y]]
	[[Category: At hook]]		[[Category: At hook]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[Category: H-n]]		[[Category: H-n]]

OCA at 19:48, 1 August 2018

OCA — Wed, 01 Aug 2018 19:48:55 GMT

←Older revision		Revision as of 19:48, 1 August 2018
Line 1:		Line 1:
		+
	==Solution structure of the C-terminal domain of Salmonella H-NS==		==Solution structure of the C-terminal domain of Salmonella H-NS==
	<StructureSection load='2l93' size='340' side='right' caption='[[2l93]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2l93' size='340' side='right' caption='[[2l93]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2l93]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L93 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2L93 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2l93]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L93 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2L93 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2l92\|2l92]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2l92\|2l92]]</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=2l93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l93 OCA], [http://pdbe.org/2l93 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2l93 RCSB], [http://www.ebi.ac.uk/pdbsum/2l93 PDBsum]</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=2l93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l93 OCA], [http://pdbe.org/2l93 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2l93 RCSB], [http://www.ebi.ac.uk/pdbsum/2l93 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2l93 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 07:10, 10 September 2015

OCA — Thu, 10 Sep 2015 07:10:46 GMT

←Older revision		Revision as of 07:10, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2l93' size='340' side='right' caption='[[2l93]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2l93' size='340' side='right' caption='[[2l93]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2l93]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar~~ typhimurium]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L93 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2L93 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2l93]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L93 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2L93 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2l92\|2l92]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2l92\|2l92]]</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=2l93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l93 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2l93 RCSB], [http://www.ebi.ac.uk/pdbsum/2l93 PDBsum]</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=2l93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l93 OCA], [http://pdbe.org/2l93 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2l93 RCSB], [http://www.ebi.ac.uk/pdbsum/2l93 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HNS_SALTY HNS_SALTY]] H-NS binds tightly to ds-DNA, increases its thermal stability and inhibits transcription. It also binds to ss-DNA and RNA but with a much lower affinity. H-NS has possible histone-like function. May be a global transcriptional regulator through its ability to bind to curved DNA sequences, which are found in regions upstream of a certain subset of promoters. It plays a role in the thermal control of pili production. It is subject to transcriptional auto-repression. It binds preferentially to the upstream region of its own gene recognizing two segments of DNA on both sides of a bend centered around -150 (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 16:
	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>
	</div>		</div>
		+	<div class="pdbe-citations 2l93" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Salmonella enterica subsp. enterica serovar~~ typhimurium]]	+	[[Category: Bacillus typhimurium loeffler 1892]]
	[[Category: Li, Y]]		[[Category: Li, Y]]
	[[Category: At hook]]		[[Category: At hook]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[Category: H-n]]		[[Category: H-n]]

OCA at 05:38, 22 December 2014

OCA — Mon, 22 Dec 2014 05:38:24 GMT

←Older revision		Revision as of 05:38, 22 December 2014
Line 2:		Line 2:
	<StructureSection load='2l93' size='340' side='right' caption='[[2l93]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2l93' size='340' side='right' caption='[[2l93]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2l93]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L93 OCA]. <br>	+	<table><tr><td colspan='2'>[[2l93]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L93 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2L93 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2l92\|2l92]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2l92\|2l92]]</td></tr>
-	<tr~~><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class~~='~~plainlinks~~'~~>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=2l93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l93 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2l93 RCSB], [http://www.ebi.ac.uk/pdbsum/2l93 PDBsum]</span></td></tr>
-	~~<tr~~><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2l93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l93 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2l93 RCSB], [http://www.ebi.ac.uk/pdbsum/2l93 PDBsum]</span></td></tr>	+	</table>
-	<table>	+
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 13:		Line 12:
	Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins.,Gordon BR, Li Y, Cote A, Weirauch MT, Ding P, Hughes TR, Navarre WW, Xia B, Liu J Proc Natl Acad Sci U S A. 2011 Jun 28;108(26):10690-5. Epub 2011 Jun 14. PMID:21673140<ref>PMID:21673140</ref>		Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins.,Gordon BR, Li Y, Cote A, Weirauch MT, Ding P, Hughes TR, Navarre WW, Xia B, Liu J Proc Natl Acad Sci U S A. 2011 Jun 28;108(26):10690-5. Epub 2011 Jun 14. PMID:21673140<ref>PMID:21673140</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	</div>		</div>
	== References ==		== References ==
Line 20:		Line 19:
	</StructureSection>		</StructureSection>
	[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]		[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
-	[[Category: Li, Y.]]	+	[[Category: Li, Y]]
	[[Category: At hook]]		[[Category: At hook]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[Category: H-n]]		[[Category: H-n]]

OCA at 09:43, 1 May 2014

OCA — Thu, 01 May 2014 09:43:10 GMT

←Older revision		Revision as of 09:43, 1 May 2014
Line 2:		Line 2:
	<StructureSection load='2l93' size='340' side='right' caption='[[2l93]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2l93' size='340' side='right' caption='[[2l93]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	[[2l93]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L93 OCA]. <br>	+	<table><tr><td colspan='2'>[[2l93]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L93 OCA]. <br>
-	<b>[[Related_structure\|Related:]]</b> [[2l92\|2l92]]<br>	+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2l92\|2l92]]</td></tr>
-	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>	+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
-	<b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2l93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l93 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2l93 RCSB], [http://www.ebi.ac.uk/pdbsum/2l93 PDBsum]</span><br>	+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2l93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l93 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2l93 RCSB], [http://www.ebi.ac.uk/pdbsum/2l93 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	H-NS and Lsr2 are nucleoid-associated proteins from Gram-negative bacteria and Mycobacteria, respectively, that play an important role in the silencing of horizontally acquired foreign DNA that is more AT-rich than the resident genome. Despite the fact that Lsr2 and H-NS proteins are dissimilar in sequence and structure, they serve apparently similar functions and can functionally complement one another. The mechanism by which these xenogeneic silencers selectively target AT-rich DNA has been enigmatic. We performed high-resolution protein binding microarray analysis to simultaneously assess the binding preference of H-NS and Lsr2 for all possible 8-base sequences. Concurrently, we performed a detailed structure-function relationship analysis of their C-terminal DNA binding domains by NMR. Unexpectedly, we found that H-NS and Lsr2 use a common DNA binding mechanism where a short loop containing a "Q/RGR" motif selectively interacts with the DNA minor groove, where the highest affinity is for AT-rich sequences that lack A-tracts. Mutations of the Q/RGR motif abolished DNA binding activity. Netropsin, a DNA minor groove-binding molecule effectively outcompeted H-NS and Lsr2 for binding to AT-rich sequences. These results provide a unified molecular mechanism to explain findings related to xenogeneic silencing proteins, including their lack of apparent sequence specificity but preference for AT-rich sequences. Our findings also suggest that structural information contained within the DNA minor groove is deciphered by xenogeneic silencing proteins to distinguish genetic material that is self from nonself.		H-NS and Lsr2 are nucleoid-associated proteins from Gram-negative bacteria and Mycobacteria, respectively, that play an important role in the silencing of horizontally acquired foreign DNA that is more AT-rich than the resident genome. Despite the fact that Lsr2 and H-NS proteins are dissimilar in sequence and structure, they serve apparently similar functions and can functionally complement one another. The mechanism by which these xenogeneic silencers selectively target AT-rich DNA has been enigmatic. We performed high-resolution protein binding microarray analysis to simultaneously assess the binding preference of H-NS and Lsr2 for all possible 8-base sequences. Concurrently, we performed a detailed structure-function relationship analysis of their C-terminal DNA binding domains by NMR. Unexpectedly, we found that H-NS and Lsr2 use a common DNA binding mechanism where a short loop containing a "Q/RGR" motif selectively interacts with the DNA minor groove, where the highest affinity is for AT-rich sequences that lack A-tracts. Mutations of the Q/RGR motif abolished DNA binding activity. Netropsin, a DNA minor groove-binding molecule effectively outcompeted H-NS and Lsr2 for binding to AT-rich sequences. These results provide a unified molecular mechanism to explain findings related to xenogeneic silencing proteins, including their lack of apparent sequence specificity but preference for AT-rich sequences. Our findings also suggest that structural information contained within the DNA minor groove is deciphered by xenogeneic silencing proteins to distinguish genetic material that is self from nonself.
Line 12:		Line 14:

	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>		From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:04, 30 April 2014

OCA — Wed, 30 Apr 2014 10:04:24 GMT

←Older revision		Revision as of 10:04, 30 April 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	[[2l93]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L93 OCA]. <br>		[[2l93]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L93 OCA]. <br>
-	<b>Related:</b> [[2l92\|2l92]]<br>	+	<b>[[Related_structure\|Related:]]</b> [[2l92\|2l92]]<br>
	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>		<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
		+	<b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2l93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l93 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2l93 RCSB], [http://www.ebi.ac.uk/pdbsum/2l93 PDBsum]</span><br>
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	H-NS and Lsr2 are nucleoid-associated proteins from Gram-negative bacteria and Mycobacteria, respectively, that play an important role in the silencing of horizontally acquired foreign DNA that is more AT-rich than the resident genome. Despite the fact that Lsr2 and H-NS proteins are dissimilar in sequence and structure, they serve apparently similar functions and can functionally complement one another. The mechanism by which these xenogeneic silencers selectively target AT-rich DNA has been enigmatic. We performed high-resolution protein binding microarray analysis to simultaneously assess the binding preference of H-NS and Lsr2 for all possible 8-base sequences. Concurrently, we performed a detailed structure-function relationship analysis of their C-terminal DNA binding domains by NMR. Unexpectedly, we found that H-NS and Lsr2 use a common DNA binding mechanism where a short loop containing a "Q/RGR" motif selectively interacts with the DNA minor groove, where the highest affinity is for AT-rich sequences that lack A-tracts. Mutations of the Q/RGR motif abolished DNA binding activity. Netropsin, a DNA minor groove-binding molecule effectively outcompeted H-NS and Lsr2 for binding to AT-rich sequences. These results provide a unified molecular mechanism to explain findings related to xenogeneic silencing proteins, including their lack of apparent sequence specificity but preference for AT-rich sequences. Our findings also suggest that structural information contained within the DNA minor groove is deciphered by xenogeneic silencing proteins to distinguish genetic material that is self from nonself.		H-NS and Lsr2 are nucleoid-associated proteins from Gram-negative bacteria and Mycobacteria, respectively, that play an important role in the silencing of horizontally acquired foreign DNA that is more AT-rich than the resident genome. Despite the fact that Lsr2 and H-NS proteins are dissimilar in sequence and structure, they serve apparently similar functions and can functionally complement one another. The mechanism by which these xenogeneic silencers selectively target AT-rich DNA has been enigmatic. We performed high-resolution protein binding microarray analysis to simultaneously assess the binding preference of H-NS and Lsr2 for all possible 8-base sequences. Concurrently, we performed a detailed structure-function relationship analysis of their C-terminal DNA binding domains by NMR. Unexpectedly, we found that H-NS and Lsr2 use a common DNA binding mechanism where a short loop containing a "Q/RGR" motif selectively interacts with the DNA minor groove, where the highest affinity is for AT-rich sequences that lack A-tracts. Mutations of the Q/RGR motif abolished DNA binding activity. Netropsin, a DNA minor groove-binding molecule effectively outcompeted H-NS and Lsr2 for binding to AT-rich sequences. These results provide a unified molecular mechanism to explain findings related to xenogeneic silencing proteins, including their lack of apparent sequence specificity but preference for AT-rich sequences. Our findings also suggest that structural information contained within the DNA minor groove is deciphered by xenogeneic silencing proteins to distinguish genetic material that is self from nonself.

OCA at 08:26, 30 April 2014

OCA — Wed, 30 Apr 2014 08:26:40 GMT

←Older revision		Revision as of 08:26, 30 April 2014
Line 1:		Line 1:
-	[[~~Image:~~2l93.~~png~~\|~~left\|200px~~]]	+	==Solution structure of the C-terminal domain of Salmonella H-NS==
		+	<StructureSection load='2l93' size='340' side='right' caption='[[2l93]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	[[2l93]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L93 OCA]. <br>
		+	<b>Related:</b> [[2l92\|2l92]]<br>
		+	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
		+	== Publication Abstract from PubMed ==
		+	H-NS and Lsr2 are nucleoid-associated proteins from Gram-negative bacteria and Mycobacteria, respectively, that play an important role in the silencing of horizontally acquired foreign DNA that is more AT-rich than the resident genome. Despite the fact that Lsr2 and H-NS proteins are dissimilar in sequence and structure, they serve apparently similar functions and can functionally complement one another. The mechanism by which these xenogeneic silencers selectively target AT-rich DNA has been enigmatic. We performed high-resolution protein binding microarray analysis to simultaneously assess the binding preference of H-NS and Lsr2 for all possible 8-base sequences. Concurrently, we performed a detailed structure-function relationship analysis of their C-terminal DNA binding domains by NMR. Unexpectedly, we found that H-NS and Lsr2 use a common DNA binding mechanism where a short loop containing a "Q/RGR" motif selectively interacts with the DNA minor groove, where the highest affinity is for AT-rich sequences that lack A-tracts. Mutations of the Q/RGR motif abolished DNA binding activity. Netropsin, a DNA minor groove-binding molecule effectively outcompeted H-NS and Lsr2 for binding to AT-rich sequences. These results provide a unified molecular mechanism to explain findings related to xenogeneic silencing proteins, including their lack of apparent sequence specificity but preference for AT-rich sequences. Our findings also suggest that structural information contained within the DNA minor groove is deciphered by xenogeneic silencing proteins to distinguish genetic material that is self from nonself.

-	<!--	+	Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins.,Gordon BR, Li Y, Cote A, Weirauch MT, Ding P, Hughes TR, Navarre WW, Xia B, Liu J Proc Natl Acad Sci U S A. 2011 Jun 28;108(26):10690-5. Epub 2011 Jun 14. PMID:21673140<ref>PMID:21673140</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_2l93"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display.~~	+
-	-->	+
-	~~{{STRUCTURE_2l93\| PDB=2l93 \| SCENE= }}~~	+

-	~~===Solution structure~~ of the ~~C-terminal domain of Salmonella H-NS===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	== References ==
-		+	<references/>
-	~~<!--~~	+	__TOC__
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21673140}}, adds the Publication Abstract to the page~~	+	</StructureSection>
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 21673140 is the PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_21673140}}~~	+
-		+
-	==~~About this Structure~~==	+
-	~~[[2l93]] is a 1 chain structure with sequence from [http:~~//en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L93 OCA].	+
-		+
-	~~==Reference==~~	+
-	<~~ref group="xtra">PMID:021673140</ref><references group="xtra"~~/>	+
	[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]		[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
	[[Category: Li, Y.]]		[[Category: Li, Y.]]