5vfy - Revision history

OCA at 14:10, 13 March 2024

OCA — Wed, 13 Mar 2024 14:10:13 GMT

←Older revision		Revision as of 14:10, 13 March 2024
Line 1:		Line 1:

	==Structure of an accessory protein of the pCW3 relaxosome==		==Structure of an accessory protein of the pCW3 relaxosome==
-	<StructureSection load='5vfy' size='340' side='right' caption='[[5vfy]], [[Resolution\|resolution]] 2.49Å' scene=''>	+	<StructureSection load='5vfy' size='340' side='right'caption='[[5vfy]], [[Resolution\|resolution]] 2.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vfy]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_perfringens"_veillon_and_zuber_1898 "bacillus~~ perfringens~~" veillon and zuber 1898~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VFY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VFY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vfy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VFY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VFY FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5vfx\|5vfx]]</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]] 2.49Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">ERS852446_03033, pBeta2_00022, pCpb2-CP1_20, pCW3_0028, pNetB-NE10_20, pNetB_00021, pTet_021 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=1502 "Bacillus perfringens" Veillon and Zuber 1898])~~</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=5vfy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vfy OCA], [https://pdbe.org/5vfy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vfy RCSB], [https://www.ebi.ac.uk/pdbsum/5vfy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vfy 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=5vfy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vfy OCA], [~~http~~://pdbe.org/5vfy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vfy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vfy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vfy ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q1PLI2_CLOPF Q1PLI2_CLOPF]
-	Conjugation is fundamental for the acquisition of new genetic traits and the development of antibiotic resistance in pathogenic organisms. Here, we show that a hypothetical Clostridium perfringens protein, TcpK, which is encoded by the tetracycline resistance plasmid pCW3, is essential for efficient conjugative DNA transfer. Our studies reveal that TcpK is a member of the winged helix-turn-helix (wHTH) transcription factor superfamily and that it forms a dimer in solution. Furthermore, TcpK specifically binds to a nine-nucleotide sequence that is present as tandem repeats within the pCW3 origin of transfer (oriT). The X-ray crystal structure of the TcpK-TcpK box complex reveals a binding mode centered on and around the beta-wing, which is different from what has been previously shown for other wHTH proteins. Structure-guided mutagenesis experiments validate the specific interaction between TcpK and the DNA molecule. ~~Additional studies highlight that the TcpK dimer is important for specific DNA binding~~.	+

-	Crystal structure of TcpK in complex with oriT DNA of the antibiotic resistance plasmid pCW3.,Traore DAK, Wisniewski JA, Flanigan SF, Conroy PJ, Panjikar S, Mok YF, Lao C, Griffin MDW, Adams V, Rood JI, Whisstock JC Nat Commun. 2018 Sep 13;9(1):3732. doi: 10.1038/s41467-018-06096-2. PMID:30213934<ref>PMID:30213934</ref>	+	==See Also==
-		+	*[[Antibody 3D structures\|Antibody 3D structures]]
-	~~From MEDLINE®/PubMed®, a database~~ of ~~the U.S. National Library~~ of ~~Medicine.<br>~~	+	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
-	~~</div>~~	+
-	~~<div class="pdbe~~-~~citations 5vfy" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ perfringens ~~veillon and zuber 1898~~]]	+	[[Category: Clostridium perfringens]]
-	[[Category: Adams, V]]	+	[[Category: Large Structures]]
-	[[Category: Conroy~~, P J~~]]	+	[[Category: Adams V]]
-	[[Category: Flanigan~~, S F~~]]	+	[[Category: Conroy PJ]]
-	[[Category: Griffin~~, M D.W~~]]	+	[[Category: Flanigan SF]]
-	[[Category: Lao, C]]	+	[[Category: Griffin MDW]]
-	[[Category: Mok, Y F]]	+	[[Category: Lao C]]
-	[[Category: Panjikar, S]]	+	[[Category: Mok Y-F]]
-	[[Category: Rood~~, J I~~]]	+	[[Category: Panjikar S]]
-	[[Category: Traore~~, D A.K~~]]	+	[[Category: Rood JI]]
-	[[Category: Whisstock~~, J C~~]]	+	[[Category: Traore DAK]]
-	[[Category: Wisniewski~~, J A]]~~	+	[[Category: Whisstock JC]]
-	~~[[Category: Clostridium perfringen]]~~	+	[[Category: Wisniewski JA]]
-	~~[[Category: Conjugation]]~~	+
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Winged helix-turn-helix~~]]	+

OCA at 08:33, 3 October 2018

OCA — Wed, 03 Oct 2018 08:33:54 GMT

←Older revision		Revision as of 08:33, 3 October 2018
Line 3:		Line 3:
	<StructureSection load='5vfy' size='340' side='right' caption='[[5vfy]], [[Resolution\|resolution]] 2.49Å' scene=''>		<StructureSection load='5vfy' size='340' side='right' caption='[[5vfy]], [[Resolution\|resolution]] 2.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vfy]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VFY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vfy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_perfringens"_veillon_and_zuber_1898 "bacillus perfringens" veillon and zuber 1898]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VFY FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vfx\|5vfx]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vfx\|5vfx]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ERS852446_03033, pBeta2_00022, pCpb2-CP1_20, pCW3_0028, pNetB-NE10_20, pNetB_00021, pTet_021 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1502 "Bacillus perfringens" Veillon and Zuber 1898])</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=5vfy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vfy OCA], [http://pdbe.org/5vfy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vfy RCSB], [http://www.ebi.ac.uk/pdbsum/5vfy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vfy 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=5vfy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vfy OCA], [http://pdbe.org/5vfy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vfy RCSB], [http://www.ebi.ac.uk/pdbsum/5vfy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vfy ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Conjugation is fundamental for the acquisition of new genetic traits and the development of antibiotic resistance in pathogenic organisms. Here, we show that a hypothetical Clostridium perfringens protein, TcpK, which is encoded by the tetracycline resistance plasmid pCW3, is essential for efficient conjugative DNA transfer. Our studies reveal that TcpK is a member of the winged helix-turn-helix (wHTH) transcription factor superfamily and that it forms a dimer in solution. Furthermore, TcpK specifically binds to a nine-nucleotide sequence that is present as tandem repeats within the pCW3 origin of transfer (oriT). The X-ray crystal structure of the TcpK-TcpK box complex reveals a binding mode centered on and around the beta-wing, which is different from what has been previously shown for other wHTH proteins. Structure-guided mutagenesis experiments validate the specific interaction between TcpK and the DNA molecule. Additional studies highlight that the TcpK dimer is important for specific DNA binding.
		+
		+	Crystal structure of TcpK in complex with oriT DNA of the antibiotic resistance plasmid pCW3.,Traore DAK, Wisniewski JA, Flanigan SF, Conroy PJ, Panjikar S, Mok YF, Lao C, Griffin MDW, Adams V, Rood JI, Whisstock JC Nat Commun. 2018 Sep 13;9(1):3732. doi: 10.1038/s41467-018-06096-2. PMID:30213934<ref>PMID:30213934</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5vfy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus perfringens veillon and zuber 1898]]
	[[Category: Adams, V]]		[[Category: Adams, V]]
	[[Category: Conroy, P J]]		[[Category: Conroy, P J]]

OCA at 05:38, 18 April 2018

OCA — Wed, 18 Apr 2018 05:38:04 GMT

←Older revision		Revision as of 05:38, 18 April 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vfy is ~~ON HOLD until Paper Publication~~	+	==Structure of an accessory protein of the pCW3 relaxosome==
-		+	<StructureSection load='5vfy' size='340' side='right' caption='[[5vfy]], [[Resolution\|resolution]] 2.49Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5vfy]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VFY FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vfx\|5vfx]]</td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5vfy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vfy OCA], [http://pdbe.org/5vfy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vfy RCSB], [http://www.ebi.ac.uk/pdbsum/5vfy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vfy ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Adams, V]]
		+	[[Category: Conroy, P J]]
		+	[[Category: Flanigan, S F]]
		+	[[Category: Griffin, M D.W]]
		+	[[Category: Lao, C]]
		+	[[Category: Mok, Y F]]
		+	[[Category: Panjikar, S]]
		+	[[Category: Rood, J I]]
		+	[[Category: Traore, D A.K]]
		+	[[Category: Whisstock, J C]]
		+	[[Category: Wisniewski, J A]]
		+	[[Category: Clostridium perfringen]]
		+	[[Category: Conjugation]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Winged helix-turn-helix]]

OCA at 12:15, 27 April 2017

OCA — Thu, 27 Apr 2017 12:15:19 GMT

←Older revision		Revision as of 12:15, 27 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 19 Apr 2017 11:23:33 GMT

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

←Older revision

Revision as of 11:23, 19 April 2017

OCA: New page: '''Unreleased structure''' The entry 5vfy is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 19 Apr 2017 11:23:32 GMT

New page: '''Unreleased structure''' The entry 5vfy is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5vfy is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]