5zux - Revision history

OCA at 07:29, 1 May 2024

OCA — Wed, 01 May 2024 07:29:17 GMT

←Older revision		Revision as of 07:29, 1 May 2024
Line 1:		Line 1:

	==Solution Structure of the DNA complex of the C-terminal Domain of Rok==		==Solution Structure of the DNA complex of the C-terminal Domain of Rok==
-	<StructureSection load='5zux' size='340' side='right'caption='[[5zux~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='5zux' size='340' side='right'caption='[[5zux]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zux]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZUX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ZUX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zux]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] and [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZUX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZUX FirstGlance]. <br>
-	</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=5zux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zux OCA], [~~http~~://pdbe.org/5zux PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zux RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zux PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zux ProSAT]</span></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=5zux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zux OCA], [https://pdbe.org/5zux PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zux RCSB], [https://www.ebi.ac.uk/pdbsum/5zux PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zux ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/ROK_BACSU ROK_BACSU] Repressor of comK, the master regulator of competence development (PubMed:11849533). Overexpression seems to be lethal (PubMed:11849533). Represses at least 20 genes that specify membrane-localized and secreted proteins, including some that encode products with antibiotic activity (PubMed:15743949). Binds to many AT-rich sites in the chromosome, many of which are known or thought to derive from horizontal gene transfer; helps keep mobile element ICEBs1 quiescent in the genome (PubMed:21085634). Binds to its own promoter and is thus probably autoregulatory (PubMed:21085634).<ref>PMID:11849533</ref> <ref>PMID:15743949</ref> <ref>PMID:21085634</ref>
-	Bacterial xenogeneic silencers play important roles in bacterial evolution by recognizing and inhibiting expression from foreign genes acquired through horizontal gene transfer, thereby buffering against potential fitness consequences of their misregulated expression. ~~Here, the detailed DNA binding properties~~ of ~~Rok~~, ~~a xenogeneic silencer in Bacillus subtilis, was studied using protein binding microarray, and~~ the ~~solution structure~~ of ~~its C-terminal DNA binding domain was determined in complex with DNA~~. ~~The C-terminal domain of Rok adopts a typical winged helix fold, with a novel DNA recognition mechanism different from other winged helix proteins or xenogeneic silencers~~. ~~Rok binds the DNA minor groove by forming hydrogen bonds to bases through N154, T156~~ at ~~the N~~-~~terminal of alpha3 helix~~ and ~~R174 of wing W1~~, ~~assisted by four lysine residues interacting electrostatically~~ with ~~DNA backbone phosphate groups~~. ~~These structural features endow Rok with preference towards DNA sequences harboring AACTA, TACTA, and flexible multiple TpA steps, while rigid A~~-~~tracts are disfavored. Correspondingly, the Bacillus genomes containing Rok are~~ rich in ~~A-tracts and show a dramatic underrepresentation~~ of ~~AACTA and TACTA,~~ which are ~~significantly enriched~~ in ~~Rok binding regions. These observations suggest that~~ the ~~xenogeneic silencing protein and its resident~~ genome ~~may have evolved cooperatively~~.	+
-		+
-	~~How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in~~ its ~~resident genome.,Duan B, Ding P, Hughes TR, Navarre WW, Liu J, Xia B Nucleic Acids Res. 2018 Sep 25. pii~~: ~~5106470~~. ~~doi: 10.1093/nar/gky836. PMID:30252102~~<ref>PMID:~~30252102~~</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.~~<br>	+
-	</~~div~~>	+
-	<~~div class="pdbe-citations 5zux" style="background-color~~:~~#fffaf0;">~~</~~div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus subtilis]]
	[[Category: Bacillus subtilis subsp. subtilis str. 168]]		[[Category: Bacillus subtilis subsp. subtilis str. 168]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Duan, B]]	+	[[Category: Duan B]]
-	[[Category: Xia, B]]	+	[[Category: Xia B]]
-	~~[[Category: Dna binding protein-dna complex]]~~	+
-	~~[[Category: Winged helix]]~~	+
-	~~[[Category: Xenogeneic silencer~~]]	+

OCA at 21:24, 28 October 2020

OCA — Wed, 28 Oct 2020 21:24:18 GMT

←Older revision		Revision as of 21:24, 28 October 2020
Line 1:		Line 1:

	==Solution Structure of the DNA complex of the C-terminal Domain of Rok==		==Solution Structure of the DNA complex of the C-terminal Domain of Rok==
-	<StructureSection load='5zux' size='340' side='right' caption='[[5zux]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='5zux' size='340' side='right'caption='[[5zux]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zux]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZUX OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZUX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zux]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZUX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZUX 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=5zux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zux OCA], [http://pdbe.org/5zux PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zux RCSB], [http://www.ebi.ac.uk/pdbsum/5zux PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zux ProSAT]</span></td></tr>	+	</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=5zux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zux OCA], [http://pdbe.org/5zux PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zux RCSB], [http://www.ebi.ac.uk/pdbsum/5zux PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zux ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus subtilis subsp. subtilis str. 168]]		[[Category: Bacillus subtilis subsp. subtilis str. 168]]
		+	[[Category: Large Structures]]
	[[Category: Duan, B]]		[[Category: Duan, B]]
	[[Category: Xia, B]]		[[Category: Xia, B]]

OCA at 07:52, 17 October 2018

OCA — Wed, 17 Oct 2018 07:52:44 GMT

←Older revision		Revision as of 07:52, 17 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zux is ~~ON HOLD until Paper~~ Publication	+	==Solution Structure of the DNA complex of the C-terminal Domain of Rok==
		+	<StructureSection load='5zux' size='340' side='right' caption='[[5zux]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zux]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZUX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZUX 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=5zux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zux OCA], [http://pdbe.org/5zux PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zux RCSB], [http://www.ebi.ac.uk/pdbsum/5zux PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zux ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial xenogeneic silencers play important roles in bacterial evolution by recognizing and inhibiting expression from foreign genes acquired through horizontal gene transfer, thereby buffering against potential fitness consequences of their misregulated expression. Here, the detailed DNA binding properties of Rok, a xenogeneic silencer in Bacillus subtilis, was studied using protein binding microarray, and the solution structure of its C-terminal DNA binding domain was determined in complex with DNA. The C-terminal domain of Rok adopts a typical winged helix fold, with a novel DNA recognition mechanism different from other winged helix proteins or xenogeneic silencers. Rok binds the DNA minor groove by forming hydrogen bonds to bases through N154, T156 at the N-terminal of alpha3 helix and R174 of wing W1, assisted by four lysine residues interacting electrostatically with DNA backbone phosphate groups. These structural features endow Rok with preference towards DNA sequences harboring AACTA, TACTA, and flexible multiple TpA steps, while rigid A-tracts are disfavored. Correspondingly, the Bacillus genomes containing Rok are rich in A-tracts and show a dramatic underrepresentation of AACTA and TACTA, which are significantly enriched in Rok binding regions. These observations suggest that the xenogeneic silencing protein and its resident genome may have evolved cooperatively.

-	~~Authors: Xia, B~~., Duan, B.	+	How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome.,Duan B, Ding P, Hughes TR, Navarre WW, Liu J, Xia B Nucleic Acids Res. 2018 Sep 25. pii: 5106470. doi: 10.1093/nar/gky836. PMID:30252102<ref>PMID:30252102</ref>

-	~~Description: Solution Structure~~ of the ~~DNA complex~~ of ~~the C-terminal Domain of Rok~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Xia, B~~]]	+	<div class="pdbe-citations 5zux" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bacillus subtilis subsp. subtilis str. 168]]
	[[Category: Duan, B]]		[[Category: Duan, B]]
		+	[[Category: Xia, B]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Winged helix]]
		+	[[Category: Xenogeneic silencer]]

OCA at 06:08, 3 October 2018

OCA — Wed, 03 Oct 2018 06:08:48 GMT

←Older revision		Revision as of 06:08, 3 October 2018
Line 3:		Line 3:
	The entry 5zux is ON HOLD until Paper Publication		The entry 5zux is ON HOLD until Paper Publication

-	Authors: Xia, B., Bo, D.	+	Authors: Xia, B., Duan, B.

	Description: Solution Structure of the DNA complex of the C-terminal Domain of Rok		Description: Solution Structure of the DNA complex of the C-terminal Domain of Rok
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Bo, D]]
	[[Category: Xia, B]]		[[Category: Xia, B]]
		+	[[Category: Duan, B]]

OCA at 03:51, 30 May 2018

OCA — Wed, 30 May 2018 03:51:53 GMT

←Older revision		Revision as of 03:51, 30 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Xia, B., Bo, D.		Authors: Xia, B., Bo, D.

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

OCA — Wed, 16 May 2018 03:54:52 GMT

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

←Older revision

Revision as of 03:54, 16 May 2018

OCA: New page: '''Unreleased structure''' The entry 5zux is ON HOLD Authors: Xia, B., Bo, D. Description: Solution Structure of the DNA complex of the C-terminal Domain of Rok [[Category: Unreleased ...

OCA — Wed, 16 May 2018 03:54:51 GMT

New page: '''Unreleased structure''' The entry 5zux is ON HOLD Authors: Xia, B., Bo, D. Description: Solution Structure of the DNA complex of the C-terminal Domain of Rok [[Category: Unreleased ...

New page

'''Unreleased structure'''

The entry 5zux is ON HOLD

Authors: Xia, B., Bo, D.

Description: Solution Structure of the DNA complex of the C-terminal Domain of Rok
[[Category: Unreleased Structures]]
[[Category: Bo, D]]
[[Category: Xia, B]]