6omf - Revision history

OCA at 14:52, 13 March 2024

2024-03-13T14:52:24Z

←Older revision		Revision as of 14:52, 13 March 2024
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	<SX load='6omf' size='340' side='right' viewer='molstar' caption='[[6omf]], [[Resolution\|resolution]] 3.26Å' scene=''>		<SX load='6omf' size='340' side='right' viewer='molstar' caption='[[6omf]], [[Resolution\|resolution]] 3.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6omf]] is a 9 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~] and [~~http~~://en.wikipedia.org/wiki/~~"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OMF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6OMF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6omf]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OMF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OMF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.26Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>rpoA, Z4665, ECs4160 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" Migula 1895]), rpoB, Z5560, ECs4910 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoC, tabB, b3988, JW3951 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoZ, Z5075, ECs4524 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoS, C2273_13580 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892]), crl ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</td><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6]~~ </~~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=6omf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6omf OCA], [https://pdbe.org/6omf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6omf RCSB], [https://www.ebi.ac.uk/pdbsum/6omf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6omf 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=6omf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6omf OCA], [~~http~~://pdbe.org/6omf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6omf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6omf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6omf ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/A0A0F7J6B7_SALTM A0A0F7J6B7_SALTM]] Binds to the sigma-S subunit of RNA polymerase, activating expression of sigma-S-regulated genes. Stimulates RNA polymerase holoenzyme formation and may bind to several other sigma factors, such as sigma-70 and sigma-32.[HAMAP-Rule:MF_01178] [[http://www.uniprot.org/uniprot/RPOC_ECOLI RPOC_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.~~[HAMAP-Rule:MF_01322] [[http://www.uniprot.org/uniprot/RPOB_ECO57 RPOB_ECO57]] DNA-dependent RNA polymerase catalyzes~~ the ~~transcription of DNA into RNA using~~ the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOA_ECO57 RPOA_ECO57]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOZ_ECO57 RPOZ_ECO57]] Promotes RNA polymerase assembly~~. Latches the N- and C-terminal regions~~ of ~~the beta' subunit thereby facilitating its interaction with the beta and alpha~~ subunits ~~(By similarity). [[http://www.uniprot.org/uniprot/S5ZIY8_SALTM S5ZIY8_SALTM]] Sigma factors are initiation factors that promote the attachment of RNA polymerase~~ to ~~specific initiation sites and are then released. This sigma factor is~~ the ~~master transcriptional regulator of the stationary phase and the general stress response~~.[HAMAP-Rule:~~MF_00959~~]	+	[https://www.uniprot.org/uniprot/RPOA_ECOLI RPOA_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme.[HAMAP-Rule:MF_00059]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	In bacteria, a primary sigma-factor associates with the core RNA polymerase (RNAP) to control most transcription initiation, while alternative sigma-factors are used to coordinate expression of additional regulons in response to environmental conditions. Many alternative sigma-factors are negatively regulated by anti-sigma-factors. In Escherichia coli, Salmonella enterica, and many other gamma-proteobacteria, the transcription factor Crl positively regulates the alternative sigma(S)-regulon by promoting the association of sigma(S) with RNAP without interacting with promoter DNA. The molecular mechanism for Crl activity is unknown. Here, we determined a single-particle cryo-electron microscopy structure of Crl-sigma(S)-RNAP in an open promoter complex with a sigma(S)-regulon promoter. In addition to previously predicted interactions between Crl and domain 2 of sigma(S) (sigma(S) 2), the structure, along with p-benzoylphenylalanine cross-linking, reveals that Crl interacts with a structural element of the RNAP beta'-subunit that we call the beta'-clamp-toe (beta'CT). Deletion of the beta'CT decreases activation by Crl without affecting basal transcription, highlighting the functional importance of the Crl-beta'CT interaction. We conclude that Crl activates sigma(S)-dependent transcription in part through stabilizing sigma(S)-RNAP by tethering sigma(S) 2 and the beta'CT. We propose that Crl, and other transcription activators that may use similar mechanisms, be designated sigma-activators.	+
-		+
-	Structural basis for transcription activation by Crl through tethering of sigma(S) and RNA polymerase.,Cartagena AJ, Banta AB, Sathyan N, Ross W, Gourse RL, Campbell EA, Darst SA Proc Natl Acad Sci U S A. 2019 Sep 17;116(38):18923-18927. doi:, 10.1073/pnas.1910827116. Epub 2019 Sep 4. PMID:31484766<ref>PMID:31484766</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6omf" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]		*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~	+	[[Category: Escherichia coli]]
-	~~[[Category: Bacillus typhimurium loeffler 1892]]~~	+
-	~~[[Category: DNA-directed RNA polymerase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Campbell, E A~~]]	+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
-	[[Category: ~~Cartagena, A Jaramillo~~]]	+	[[Category: Campbell EA]]
-	[[Category: Darst~~, S A~~]]	+	[[Category: Darst SA]]
-	[[Category: ~~Betass']]~~	+	[[Category: Jaramillo Cartagena A]]
-	~~[[Category: Dna/rna]]~~	+
-	~~[[Category: Sigma]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription-activator]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 04:06, 11 April 2020

2020-04-11T04:06:30Z

←Older revision		Revision as of 04:06, 11 April 2020
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	<SX load='6omf' size='340' side='right' viewer='molstar' caption='[[6omf]], [[Resolution\|resolution]] 3.26Å' scene=''>		<SX load='6omf' size='340' side='right' viewer='molstar' caption='[[6omf]], [[Resolution\|resolution]] 3.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6omf]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OMF OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6OMF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6omf]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OMF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6OMF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoA, Z4665, ECs4160 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoB, Z5560, ECs4910 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoC, tabB, b3988, JW3951 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoZ, Z5075, ECs4524 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoS, C2273_13580 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892]), crl ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoA, Z4665, ECs4160 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoB, Z5560, ECs4910 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoC, tabB, b3988, JW3951 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoZ, Z5075, ECs4524 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoS, C2273_13580 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892]), crl ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </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=6omf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6omf OCA], [http://pdbe.org/6omf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6omf RCSB], [http://www.ebi.ac.uk/pdbsum/6omf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6omf 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=6omf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6omf OCA], [http://pdbe.org/6omf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6omf RCSB], [http://www.ebi.ac.uk/pdbsum/6omf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6omf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 23:15, 6 March 2020

2020-03-06T23:15:50Z

←Older revision		Revision as of 23:15, 6 March 2020
Line 1:		Line 1:

	==CryoEM structure of SigmaS-transcription initiation complex with activator Crl==		==CryoEM structure of SigmaS-transcription initiation complex with activator Crl==
-	<~~StructureSection~~ load='6omf' size='340' side='right'caption='[[6omf]], [[Resolution\|resolution]] 3.26Å' scene=''>	+	<SX load='6omf' size='340' side='right' viewer='molstar' caption='[[6omf]], [[Resolution\|resolution]] 3.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6omf]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OMF FirstGlance]. <br>		<table><tr><td colspan='2'>[[6omf]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OMF FirstGlance]. <br>
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 6omf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6omf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Bacillus typhimurium loeffler 1892]]		[[Category: Bacillus typhimurium loeffler 1892]]

OCA at 11:16, 2 October 2019

2019-10-02T11:16:08Z

←Older revision		Revision as of 11:16, 2 October 2019
Line 3:		Line 3:
	<StructureSection load='6omf' size='340' side='right'caption='[[6omf]], [[Resolution\|resolution]] 3.26Å' scene=''>		<StructureSection load='6omf' size='340' side='right'caption='[[6omf]], [[Resolution\|resolution]] 3.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6omf]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OMF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6omf]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OMF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoA, Z4665, ECs4160 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoB, Z5560, ECs4910 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoC, tabB, b3988, JW3951 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoZ, Z5075, ECs4524 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoS, C2273_13580 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892]), crl ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </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=6omf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6omf OCA], [http://pdbe.org/6omf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6omf RCSB], [http://www.ebi.ac.uk/pdbsum/6omf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6omf 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=6omf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6omf OCA], [http://pdbe.org/6omf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6omf RCSB], [http://www.ebi.ac.uk/pdbsum/6omf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6omf ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/A0A0F7J6B7_SALTM A0A0F7J6B7_SALTM]] Binds to the sigma-S subunit of RNA polymerase, activating expression of sigma-S-regulated genes. Stimulates RNA polymerase holoenzyme formation and may bind to several other sigma factors, such as sigma-70 and sigma-32.[HAMAP-Rule:MF_01178] [[http://www.uniprot.org/uniprot/RPOC_ECOLI RPOC_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] [[http://www.uniprot.org/uniprot/RPOB_ECO57 RPOB_ECO57]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOA_ECO57 RPOA_ECO57]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOZ_ECO57 RPOZ_ECO57]] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits (By similarity). [[http://www.uniprot.org/uniprot/S5ZIY8_SALTM S5ZIY8_SALTM]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the master transcriptional regulator of the stationary phase and the general stress response.[HAMAP-Rule:MF_00959]		[[http://www.uniprot.org/uniprot/A0A0F7J6B7_SALTM A0A0F7J6B7_SALTM]] Binds to the sigma-S subunit of RNA polymerase, activating expression of sigma-S-regulated genes. Stimulates RNA polymerase holoenzyme formation and may bind to several other sigma factors, such as sigma-70 and sigma-32.[HAMAP-Rule:MF_01178] [[http://www.uniprot.org/uniprot/RPOC_ECOLI RPOC_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] [[http://www.uniprot.org/uniprot/RPOB_ECO57 RPOB_ECO57]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOA_ECO57 RPOA_ECO57]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOZ_ECO57 RPOZ_ECO57]] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits (By similarity). [[http://www.uniprot.org/uniprot/S5ZIY8_SALTM S5ZIY8_SALTM]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the master transcriptional regulator of the stationary phase and the general stress response.[HAMAP-Rule:MF_00959]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In bacteria, a primary sigma-factor associates with the core RNA polymerase (RNAP) to control most transcription initiation, while alternative sigma-factors are used to coordinate expression of additional regulons in response to environmental conditions. Many alternative sigma-factors are negatively regulated by anti-sigma-factors. In Escherichia coli, Salmonella enterica, and many other gamma-proteobacteria, the transcription factor Crl positively regulates the alternative sigma(S)-regulon by promoting the association of sigma(S) with RNAP without interacting with promoter DNA. The molecular mechanism for Crl activity is unknown. Here, we determined a single-particle cryo-electron microscopy structure of Crl-sigma(S)-RNAP in an open promoter complex with a sigma(S)-regulon promoter. In addition to previously predicted interactions between Crl and domain 2 of sigma(S) (sigma(S) 2), the structure, along with p-benzoylphenylalanine cross-linking, reveals that Crl interacts with a structural element of the RNAP beta'-subunit that we call the beta'-clamp-toe (beta'CT). Deletion of the beta'CT decreases activation by Crl without affecting basal transcription, highlighting the functional importance of the Crl-beta'CT interaction. We conclude that Crl activates sigma(S)-dependent transcription in part through stabilizing sigma(S)-RNAP by tethering sigma(S) 2 and the beta'CT. We propose that Crl, and other transcription activators that may use similar mechanisms, be designated sigma-activators.
		+
		+	Structural basis for transcription activation by Crl through tethering of sigma(S) and RNA polymerase.,Cartagena AJ, Banta AB, Sathyan N, Ross W, Gourse RL, Campbell EA, Darst SA Proc Natl Acad Sci U S A. 2019 Sep 17;116(38):18923-18927. doi:, 10.1073/pnas.1910827116. Epub 2019 Sep 4. PMID:31484766<ref>PMID:31484766</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6omf" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
		+	[[Category: Bacillus typhimurium loeffler 1892]]
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 15:32, 28 August 2019

2019-08-28T15:32:27Z

←Older revision		Revision as of 15:32, 28 August 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6omf is ~~ON HOLD until Paper Publication~~	+	==CryoEM structure of SigmaS-transcription initiation complex with activator Crl==
-		+	<StructureSection load='6omf' size='340' side='right'caption='[[6omf]], [[Resolution\|resolution]] 3.26Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6omf]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OMF FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </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=6omf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6omf OCA], [http://pdbe.org/6omf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6omf RCSB], [http://www.ebi.ac.uk/pdbsum/6omf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6omf ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A0F7J6B7_SALTM A0A0F7J6B7_SALTM]] Binds to the sigma-S subunit of RNA polymerase, activating expression of sigma-S-regulated genes. Stimulates RNA polymerase holoenzyme formation and may bind to several other sigma factors, such as sigma-70 and sigma-32.[HAMAP-Rule:MF_01178] [[http://www.uniprot.org/uniprot/RPOC_ECOLI RPOC_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] [[http://www.uniprot.org/uniprot/RPOB_ECO57 RPOB_ECO57]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOA_ECO57 RPOA_ECO57]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOZ_ECO57 RPOZ_ECO57]] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits (By similarity). [[http://www.uniprot.org/uniprot/S5ZIY8_SALTM S5ZIY8_SALTM]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the master transcriptional regulator of the stationary phase and the general stress response.[HAMAP-Rule:MF_00959]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Large Structures]]
		+	[[Category: Campbell, E A]]
		+	[[Category: Cartagena, A Jaramillo]]
		+	[[Category: Darst, S A]]
		+	[[Category: Betass']]
		+	[[Category: Dna/rna]]
		+	[[Category: Sigma]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription-activator]]
		+	[[Category: Transferase-dna complex]]

OCA at 04:19, 24 July 2019

2019-07-24T04:19:36Z

←Older revision		Revision as of 04:19, 24 July 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6omf is ON HOLD	+	The entry 6omf is ON HOLD until Paper Publication

	Authors:		Authors:

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

2019-04-24T05:05:57Z

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

←Older revision

Revision as of 05:05, 24 April 2019

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

2019-04-24T05:05:56Z

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

New page

'''Unreleased structure'''

The entry 6omf is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]