2n5g - Revision history

OCA at 10:20, 15 March 2023

OCA — Wed, 15 Mar 2023 10:20:13 GMT

←Older revision		Revision as of 10:20, 15 March 2023
Line 1:		Line 1:

	==NMR structure of KorA, a plasmid-encoded, global transcription regulator KorA==		==NMR structure of KorA, a plasmid-encoded, global transcription regulator KorA==
-	<StructureSection load='2n5g' size='340' side='right'caption='[[2n5g~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='2n5g' size='340' side='right'caption='[[2n5g]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2n5g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N5G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2N5G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2n5g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N5G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2N5G 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;'>[[5ckt\|5ckt]], [[5cm3\|5cm3]], [[5clv\|5clv]]</div></td></tr>	+	</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=2n5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n5g OCA], [https://pdbe.org/2n5g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2n5g RCSB], [https://www.ebi.ac.uk/pdbsum/2n5g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2n5g ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trfB, korA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2n5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n5g OCA], [https://pdbe.org/2n5g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2n5g RCSB], [https://www.ebi.ac.uk/pdbsum/2n5g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2n5g ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/KORA2_ECOLX KORA2_ECOLX]] In conjunction with KorB, inhibits the transcription of kilA, trfA and korAB operons. In conjunction with KorC is responsible for the negative control of kilC and kilE operons.	+	[https://www.uniprot.org/uniprot/KORA2_ECOLX KORA2_ECOLX] In conjunction with KorB, inhibits the transcription of kilA, trfA and korAB operons. In conjunction with KorC is responsible for the negative control of kilC and kilE operons.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bingle~~, L E~~]]	+	[[Category: Bingle LE]]
-	[[Category: Dancea~~, F V~~]]	+	[[Category: Dancea FV]]
-	[[Category: Harris, S]]	+	[[Category: Harris S]]
-	[[Category: Hyde~~, E I~~]]	+	[[Category: Hyde EI]]
-	[[Category: Lovering~~, A L~~]]	+	[[Category: Lovering AL]]
-	[[Category: Rajasekar~~, K V~~]]	+	[[Category: Rajasekar KV]]
-	[[Category: Roessle, M]]	+	[[Category: Roessle M]]
-	[[Category: Scott~~, D J~~]]	+	[[Category: Scott DJ]]
-	[[Category: Thomas~~, C M~~]]	+	[[Category: Thomas CM]]
-	[[Category: White~~, S A]]~~	+	[[Category: White SA]]
-	~~[[Category: Transcription~~]]	+

OCA at 15:40, 8 June 2021

OCA — Tue, 08 Jun 2021 15:40:19 GMT

←Older revision		Revision as of 15:40, 8 June 2021
Line 1:		Line 1:

	==NMR structure of KorA, a plasmid-encoded, global transcription regulator KorA==		==NMR structure of KorA, a plasmid-encoded, global transcription regulator KorA==
-	<StructureSection load='2n5g' size='340' side='right' caption='[[2n5g]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='2n5g' size='340' side='right'caption='[[2n5g]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2n5g]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N5G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2N5G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2n5g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N5G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2N5G FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ckt\|5ckt]], [[5cm3\|5cm3]], [[5clv\|5clv]]</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;'>[[5ckt\|5ckt]], [[5cm3\|5cm3]], [[5clv\|5clv]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trfB, korA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trfB, korA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2n5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n5g OCA], [~~http~~://pdbe.org/2n5g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2n5g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2n5g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2n5g 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=2n5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n5g OCA], [https://pdbe.org/2n5g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2n5g RCSB], [https://www.ebi.ac.uk/pdbsum/2n5g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2n5g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/KORA2_ECOLX KORA2_ECOLX]] In conjunction with KorB, inhibits the transcription of kilA, trfA and korAB operons. In conjunction with KorC is responsible for the negative control of kilC and kilE operons.	+	[[https://www.uniprot.org/uniprot/KORA2_ECOLX KORA2_ECOLX]] In conjunction with KorB, inhibits the transcription of kilA, trfA and korAB operons. In conjunction with KorC is responsible for the negative control of kilC and kilE operons.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Bingle, L E]]		[[Category: Bingle, L E]]
	[[Category: Dancea, F V]]		[[Category: Dancea, F V]]

OCA at 17:21, 15 August 2018

OCA — Wed, 15 Aug 2018 17:21:33 GMT

←Older revision		Revision as of 17:21, 15 August 2018
Line 3:		Line 3:
	<StructureSection load='2n5g' size='340' side='right' caption='[[2n5g]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2n5g' size='340' side='right' caption='[[2n5g]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2n5g]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N5G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2N5G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2n5g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N5G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2N5G FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ckt\|5ckt]], [[5cm3\|5cm3]], [[5clv\|5clv]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ckt\|5ckt]], [[5cm3\|5cm3]], [[5clv\|5clv]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trfB, korA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2n5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n5g OCA], [http://pdbe.org/2n5g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2n5g RCSB], [http://www.ebi.ac.uk/pdbsum/2n5g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2n5g 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=2n5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n5g OCA], [http://pdbe.org/2n5g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2n5g RCSB], [http://www.ebi.ac.uk/pdbsum/2n5g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2n5g ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Bingle, L E]]		[[Category: Bingle, L E]]
	[[Category: Dancea, F V]]		[[Category: Dancea, F V]]

OCA at 15:12, 26 July 2016

OCA — Tue, 26 Jul 2016 15:12:54 GMT

←Older revision		Revision as of 15:12, 26 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 2n5g is ~~ON HOLD until Paper~~ Publication	+	==NMR structure of KorA, a plasmid-encoded, global transcription regulator KorA==
		+	<StructureSection load='2n5g' size='340' side='right' caption='[[2n5g]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2n5g]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N5G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2N5G FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ckt\|5ckt]], [[5cm3\|5cm3]], [[5clv\|5clv]]</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=2n5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n5g OCA], [http://pdbe.org/2n5g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2n5g RCSB], [http://www.ebi.ac.uk/pdbsum/2n5g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2n5g ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KORA2_ECOLX KORA2_ECOLX]] In conjunction with KorB, inhibits the transcription of kilA, trfA and korAB operons. In conjunction with KorC is responsible for the negative control of kilC and kilE operons.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The IncP (Incompatibility group P) plasmids are important carriers in the spread of antibiotic resistance across Gram-negative bacteria. Gene expression in the IncP-1 plasmids is stringently controlled by a network of four global repressors, KorA, KorB, TrbA and KorC interacting cooperatively. Intriguingly, KorA and KorB can act as co-repressors at varying distances between their operators, even when they are moved to be on opposite sides of the DNA. KorA is a homodimer with the 101-amino acid subunits, folding into an N-terminal DNA-binding domain and a C-terminal dimerization domain. In this study, we have determined the structures of the free KorA repressor and two complexes each bound to a 20-bp palindromic DNA duplex containing its consensus operator sequence. Using a combination of X-ray crystallography, nuclear magnetic resonance spectroscopy, SAXS and molecular dynamics calculations, we show that the linker between the two domains is very flexible and the protein remains highly mobile in the presence of DNA. This flexibility allows the DNA-binding domains of the dimer to straddle the operator DNA on binding and is likely to be important in cooperative binding to KorB. Unexpectedly, the C-terminal domain of KorA is structurally similar to the dimerization domain of the tumour suppressor p53.

-	~~Authors: Rajasekar~~, ~~K.V~~., Lovering~~, A.L.~~, Dancea, F~~.V.~~, Scott~~, D.J.~~, Harris~~, S.~~, Bingle~~, L.E.~~, Roessle, M., Thomas~~, C.M.~~, Hyde, E.I.~~, White, S.A~~.	+	Flexibility of KorA, a plasmid-encoded, global transcription regulator, in the presence and the absence of its operator.,Rajasekar KV, Lovering AL, Dancea F, Scott DJ, Harris SA, Bingle LE, Roessle M, Thomas CM, Hyde EI, White SA Nucleic Acids Res. 2016 Mar 25. pii: gkw191. PMID:27016739<ref>PMID:27016739</ref>

-	~~Description: NMR structure of KorA~~, a ~~plasmid~~-~~encoded, global transcription regulator KorA~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Lovering~~, ~~A.L~~]]	+	<div class="pdbe-citations 2n5g" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bingle, L E]]
		+	[[Category: Dancea, F V]]
	[[Category: Harris, S]]		[[Category: Harris, S]]
-	[[Category: ~~Rajasekar~~, ~~K.V~~]]	+	[[Category: Hyde, E I]]
-	[[Category: ~~Scott~~, ~~D.J~~]]	+	[[Category: Lovering, A L]]
		+	[[Category: Rajasekar, K V]]
	[[Category: Roessle, M]]		[[Category: Roessle, M]]
-	[[Category: ~~White~~, ~~S.A~~]]	+	[[Category: Scott, D J]]
-	[[Category: ~~Bingle~~, ~~L.E~~]]	+	[[Category: Thomas, C M]]
-	[[Category: ~~Hyde~~, ~~E.I~~]]	+	[[Category: White, S A]]
-	[[Category: ~~Thomas, C.M]]~~	+	[[Category: Transcription]]
-	~~[[Category: Dancea, F.V~~]]	+

OCA: Protected "2n5g" [edit=sysop:move=sysop]

OCA — Wed, 29 Jul 2015 08:57:08 GMT

Protected "2n5g" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:57, 29 July 2015

OCA: New page: '''Unreleased structure''' The entry 2n5g is ON HOLD until Paper Publication Authors: Rajasekar, K.V., Lovering, A.L., Dancea, F.V., Scott, D.J., Harris, S., Bingle, L.E., Roessle, M., ...

OCA — Wed, 29 Jul 2015 08:57:06 GMT

New page: '''Unreleased structure''' The entry 2n5g is ON HOLD until Paper Publication Authors: Rajasekar, K.V., Lovering, A.L., Dancea, F.V., Scott, D.J., Harris, S., Bingle, L.E., Roessle, M., ...

New page

'''Unreleased structure'''

The entry 2n5g is ON HOLD until Paper Publication

Authors: Rajasekar, K.V., Lovering, A.L., Dancea, F.V., Scott, D.J., Harris, S., Bingle, L.E., Roessle, M., Thomas, C.M., Hyde, E.I., White, S.A.

Description: NMR structure of KorA, a plasmid-encoded, global transcription regulator KorA
[[Category: Unreleased Structures]]
[[Category: Lovering, A.L]]
[[Category: Harris, S]]
[[Category: Rajasekar, K.V]]
[[Category: Scott, D.J]]
[[Category: Roessle, M]]
[[Category: White, S.A]]
[[Category: Bingle, L.E]]
[[Category: Hyde, E.I]]
[[Category: Thomas, C.M]]
[[Category: Dancea, F.V]]