CtsR - Revision history

Jstuelk: /* Biological materials */

2015-06-15T14:39:21Z

‎Biological materials

134.76.70.252 at 11:38, 8 April 2014

2014-04-08T11:38:35Z

134.76.38.147 at 12:47, 2 April 2014

2014-04-02T12:47:57Z

134.76.70.252 at 09:59, 7 January 2014

2014-01-07T09:59:30Z

134.76.70.252 at 14:59, 11 November 2013

2013-11-11T14:59:37Z

134.76.70.252 at 12:20, 16 May 2013

2013-05-16T12:20:34Z

134.76.70.252 at 09:13, 14 May 2013

2013-05-14T09:13:59Z

134.76.70.252 at 11:57, 13 May 2013

2013-05-13T11:57:06Z

Jstuelk at 11:36, 14 March 2013

2013-03-14T11:36:34Z

Jstuelk at 12:47, 5 February 2013

2013-02-05T12:47:25Z

← Older revision		Revision as of 14:39, 15 June 2015
Line 1:		Line 1:
−	* '''Description:~~''' transcription repressor of class III heat shock genes (''[[clpC]]'' operon, ''[[clpE]]'', ''[[clpP]]'') <br/><br/>~~	+	{{#bank: CtsR}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''ctsR''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yacG ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| transcription repressor~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| regulation of protein degradation~~
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00830 ctsR]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=CtsR CtsR]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Regulatory function and regulation of this protein in [[SubtiPathways\|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=ctsR ctsR]'''
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Metabolic function and regulation of this protein in [[SubtiPathways\|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=CtsR CtsR]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 17 kDa, 9.261~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 462 bp, 154 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[rrnW-5S]]'', ''[[mcsA]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00830 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00830 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00830 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ctsR_context.gif]]~~
−	~~<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>~~
−	\|-
−	\|colspan="2" \|'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ctsR_101449_101913_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ctsR_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00830]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[proteolysis]]}},~~
−	~~{{SubtiWiki category\|[[transcription factors and their control]]}},~~
−	~~{{SubtiWiki category\|[[general stress proteins (controlled by SigB)]]}},~~
−	~~{{SubtiWiki category\|[[heat shock proteins]]}},~~
−	~~{{SubtiWiki category\|[[phosphoproteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CtsR regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SigB regulon]]}}~~
−	~~=The [[CtsR regulon]]=~~
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU00830
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00830&redirect=T BSU00830]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ctsR-mcsAB-clpC-radA-yacK.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10145]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' ctsR family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−	** phosphorylation of a tyrosine residue by [[McsB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/14984053 PubMed]
−	** recently, it was reported that CtsR is phosphorylated by [[McsB]] on Arg-62 rather than on a tyrosine residue [http://www.ncbi.nlm.nih.gov/sites/entrez/19498169 PubMed]
−	** in addition, Arg-15 was reported to be a phosphorylation site {{PubMed\|22517742}}
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−	** CtsR is inactivated by heat, heat sensing requires Gly-64 {{PubMed\|20852588}}
−	** non-phosphorylated [[McsB]] targets CtsR for degradation {{PubMed\|20852588}}
−	** regulated proteolysis by [[ClpP]]/[[ClpC]] {{PubMed\|11179229,16163393,17380125}}
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[McsA]]-[[McsB]]-[[CtsR]]
−	** [[CtsR]]-[[ClpP]]/[[ClpC]] (degradation of [[CtsR]]) {{PubMed\|11179229,16163393,17380125}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00830&redirect=T BSU00830]
−
−	* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3H0D 3H0D] (complex with a 26bp DNA duplex, from ''Geobacillus stearothermophilus'') {{PubMed\|19498169}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P37568 P37568]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00830]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[ctsR]]-[[mcsA]]-[[mcsB]]-[[clpC]]-[[radA]]-[[disA]]'' [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed]
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ctsR_101449_101913_1 ctsR] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed], [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed1] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed2]
−
−	* '''Regulation:'''
−	** induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
−	** repressed at low temperatures ([[CtsR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/9987115 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[CtsR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/9987115 PubMed]
−
−	* '''Additional information:''' the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
−
−	~~=Biological materials =~~
−
−	* '''Mutant:''' ''ctsR::aphA3'' availbale from the Gerth lab
−	~~ctsRG65P::spec available from the Gerth lab~~
−
−	* '''Expression vector:''' for expression, purification in E. coli with N-terminal His-tag, pRSETA available in Gerth lab
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:''' available in Gerth lab
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~'''Additional reviews:''' {{PubMed\|23479438}}~~
−	~~<pubmed>14984053 21078442 23375660</pubmed>~~
−	~~==Original publications==~~
−	~~'''Additional publications:''' {{PubMed\|17380125,16163393,19498169}}~~
−	~~<pubmed>8793870, 9987115,12923084,11717291,16788169,11069659, 9852015,12884008,8195092,9987115,11544224 9852015, 11179229, 8793870 , 12884008 21208299 20852588 22247503 22517742</pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

@@ Line 19: / Line 19: @@
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Regulatory function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=ctsR ctsR]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 9.261

@@ Line 61: / Line 61: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ctsR-mcsAB-clpC-radA-yacK.html]
@@ Line 103: / Line 104: @@
 === Database entries ===
 * '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3H0D 3H0D] (complex with a 26bp DNA duplex, from ''Geobacillus stearothermophilus'') {{PubMed|19498169}}

@@ Line 18: / Line 18: @@
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=CtsR CtsR]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulatory function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress], [http://subtiwiki.uni-goettingen.de/pathways/phosphorelay.html Phosphorelay]'''
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulatory function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=ctsR ctsR]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 9.261

@@ Line 16: / Line 16: @@
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00830 ctsR]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/CtsR CtsR]
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=CtsR CtsR]
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Regulatory function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress], [http://subtiwiki.uni-goettingen.de/pathways/phosphorelay.html Phosphorelay]'''

@@ Line 31: / Line 31: @@
   <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 |-
-|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ctsR_101449_101913_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ctsR_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ctsR_101449_101913_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ctsR_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00830]]
 |-
 |}

@@ Line 26: / Line 26: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rrnW-5S]]'', ''[[mcsA]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00830 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00830 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00830 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00830 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00830 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00830 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ctsR_context.gif]]

@@ Line 152: / Line 152: @@
 =References=
 ==Reviews==
 <pubmed>14984053 21078442 23375660</pubmed>
 ==Original publications==
 '''Additional publications:''' {{PubMed|17380125,16163393,19498169}}
 <pubmed>8793870, 9987115,12923084,11717291,16788169,11069659, 9852015,12884008,8195092,9987115,11544224 9852015, 11179229, 8793870 , 12884008 21208299 20852588 22247503 22517742</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 39: / Line 39: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 124: / Line 120: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ctsR_101449_101913_1 ctsR] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed], [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed1] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed2]
+* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed], [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed1] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed2]
 * '''Regulation:'''
@@ Line 156: / Line 152: @@
 =References=
 ==Reviews==
-<pubmed>14984053 21078442 </pubmed>
+<pubmed>14984053 21078442 23375660</pubmed>
 ==Original publications==