MtrB - Revision history

Jstuelk: /* Original Publications */

2015-01-13T10:23:14Z

‎Original Publications

134.76.70.252 at 09:33, 17 April 2014

2014-04-17T09:33:07Z

134.76.38.147 at 14:04, 2 April 2014

2014-04-02T14:04:16Z

Jstuelk at 10:39, 2 April 2014

2014-04-02T10:39:01Z

Jstuelk at 10:36, 2 April 2014

2014-04-02T10:36:17Z

Jstuelk at 16:20, 28 February 2014

2014-02-28T16:20:07Z

Jstuelk: /* Original Publications */

2014-02-28T16:16:42Z

‎Original Publications

Jstuelk at 17:30, 9 February 2014

2014-02-09T17:30:46Z

134.76.70.252 at 11:05, 7 January 2014

2014-01-07T11:05:37Z

134.76.70.252 at 08:43, 12 November 2013

2013-11-12T08:43:40Z

← Older revision		Revision as of 10:23, 13 January 2015
Line 1:		Line 1:
−	* '''Description:~~''' tryptophan operon RNA-binding attenuation protein (TRAP), controls the [[RNA switch]] in front of genes involved in biosynthesis and acquisition of tryptophan <br/><br/>~~	+	{{#bank: MtrB}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''mtrB''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| tryptophan operon RNA-binding attenuation protein (TRAP)~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| regulation of tryptophan biosynthesis<br/>(and translation) attenuation in the trp operon;<br/>repression of the folate operon~~
−	\|-
−	\|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=BSU22770 mtrB]
−	\|-
−	\|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=MtrB TRAP]
−	\|-
−	\|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=mtrB mtrB]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 8 kDa, 7.333~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 225 bp, 75 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[hepS]]'', ''[[folE]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU22770 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU22770 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU22770 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:mtrB_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=mtrB_2384534_2384761_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:mtrB_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU22770]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[biosynthesis/ acquisition of amino acids]]}},~~
−	~~{{SubtiWiki category\|[[transcription factors and their control]]}},~~
−	~~{{SubtiWiki category\|[[RNA binding regulators]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~= The [[TRAP regulon]] =~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU22770
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU22770&redirect=T BSU22770]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/mtrAB.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10278]
−
−	~~=== Additional information===~~
−	* mutations in ''[[mtrB]]'', ''[[sigB]]'', ''[[rpoB]]'', and ''[[rpoC]]'' allow ''B. subtilis'' to grow with 4-fluorotryptophan rather than with tryptophan as a canonical amino acid of the genetic code {{PubMed\|24572018}}
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' prpD family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−	** binding of tryptophan results RNA binding and thus in transcription termination
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** forms 11-mers
−	** [[MtrB\|TRAP]]<sub>11</sub>-[[RtpA]]<sub>3</sub> {{PubMed\|24682818,11557884}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU22770&redirect=T BSU22770]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=3AQD 3AQD], [http://www.rcsb.org/pdb/explore.do?structureId=1WAP 1WAP] (complex with L-tryptophan), [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2ZP9 2ZP9] (complex with [[RtpA]])
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P19466 P19466]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU22770]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[folE]]-[[mtrB]]'' {{PubMed\|2123343}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mtrB_2384534_2384761_-1 mtrB] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|2123343}}
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 331 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 599 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>19385727, 16285852, 15063849 </pubmed>~~
−
−	~~==Original Publications==~~
−	<pubmed> 22970197 19033375, 17881743 10660627 10714985 12963367 14702295 16879415 17114058 17114263 11805104,7525975,10735881,15262953,14976255,8647825,18334255,10499579,7715723,8932308,11214184,15743934,7515880,9242649,7759487,15050822,14687568,9245598,9765233,11914485,15099736,7678334,8643393,15588817,16738132,1551827,17555767,7544009,11786553,11566976,2123343,11557884,12133840,16784236,10369778,7715723 10499579 11566976 7515880, 21097886 21984911 24505391 24572018 24682818 </pubmed>
−
−	~~[[Category:Protein-coding genes]]~~

← Older revision		Revision as of 09:33, 17 April 2014
Line 122:		Line 122:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 331 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 599 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 58: / Line 58: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/mtrAB.html]
@@ Line 96: / Line 97: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=3AQD 3AQD],  [http://www.rcsb.org/pdb/explore.do?structureId=1WAP 1WAP] (complex with L-tryptophan), [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2ZP9 2ZP9] (complex with [[RtpA]])

@@ Line 47: / Line 47: @@
 = This gene is a member of the following [[regulons]] =
+= The [[TRAP regulon]] =
 =The gene=
@@ Line 75: / Line 75: @@
 * '''Paralogous protein(s):'''
 === Extended information on the protein ===

@@ Line 97: / Line 97: @@
 * '''[[SubtInteract|Interactions]]:'''
 ** forms 11-mers
-** [[MtrB|TRAP]]-[[RtpA]] {{PubMed|11557884}}
+** [[MtrB|TRAP]]<sub>11</sub>-[[RtpA]]<sub>3</sub> {{PubMed|24682818,11557884}}
 * '''[[Localization]]:'''
@@ Line 150: / Line 150: @@
 ==Original Publications==
-<pubmed> 22970197 19033375, 17881743 10660627 10714985 12963367 14702295 16879415 17114058 17114263 11805104,7525975,10735881,15262953,14976255,8647825,18334255,10499579,7715723,8932308,11214184,15743934,7515880,9242649,7759487,15050822,14687568,9245598,9765233,11914485,15099736,7678334,8643393,15588817,16738132,1551827,17555767,7544009,11786553,11566976,2123343,11557884,12133840,16784236,10369778,7715723 10499579 11566976 7515880, 21097886 21984911 24505391 24572018 </pubmed>
+<pubmed> 22970197 19033375, 17881743 10660627 10714985 12963367 14702295 16879415 17114058 17114263 11805104,7525975,10735881,15262953,14976255,8647825,18334255,10499579,7715723,8932308,11214184,15743934,7515880,9242649,7759487,15050822,14687568,9245598,9765233,11914485,15099736,7678334,8643393,15588817,16738132,1551827,17555767,7544009,11786553,11566976,2123343,11557884,12133840,16784236,10369778,7715723 10499579 11566976 7515880, 21097886 21984911 24505391 24572018 24682818 </pubmed>
 [[Category:Protein-coding genes]]

← Older revision		Revision as of 16:20, 28 February 2014
Line 64:		Line 64:

	=== Additional information===		=== Additional information===
		+	* mutations in ''[[mtrB]]'', ''[[sigB]]'', ''[[rpoB]]'', and ''[[rpoC]]'' allow ''B. subtilis'' to grow with 4-fluorotryptophan rather than with tryptophan as a canonical amino acid of the genetic code {{PubMed\|24572018}}

	=The protein=		=The protein=

@@ Line 39: / Line 39: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 85: / Line 85: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 118: / Line 118: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mtrB_2384534_2384761_-1 mtrB] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] {{PubMed|2123343}}
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|2123343}}
 * '''Regulation:'''
@@ Line 149: / Line 149: @@
 ==Original Publications==
-<pubmed> 22970197 19033375, 17881743 10660627 10714985 12963367 14702295 16879415 17114058 17114263 11805104,7525975,10735881,15262953,14976255,8647825,18334255,10499579,7715723,8932308,11214184,15743934,7515880,9242649,7759487,15050822,14687568,9245598,9765233,11914485,15099736,7678334,8643393,15588817,16738132,1551827,17555767,7544009,11786553,11566976,2123343,11557884,12133840,16784236,10369778,7715723 10499579 11566976 7515880, 21097886 21984911 </pubmed>
+<pubmed> 22970197 19033375, 17881743 10660627 10714985 12963367 14702295 16879415 17114058 17114263 11805104,7525975,10735881,15262953,14976255,8647825,18334255,10499579,7715723,8932308,11214184,15743934,7515880,9242649,7759487,15050822,14687568,9245598,9765233,11914485,15099736,7678334,8643393,15588817,16738132,1551827,17555767,7544009,11786553,11566976,2123343,11557884,12133840,16784236,10369778,7715723 10499579 11566976 7515880, 21097886 21984911 24505391 </pubmed>
 [[Category:Protein-coding genes]]

@@ 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=MtrB TRAP]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/phenyl_tyr_tryp.html Phe, Tyr, Trp], [http://subtiwiki.uni-goettingen.de/pathways/folate_biosynthesis.html Folate]'''
+|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=mtrB mtrB]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 8 kDa, 7.333

@@ 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=BSU22770 mtrB]
 |-
-|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/MtrB TRAP]
+|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=MtrB TRAP]
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/phenyl_tyr_tryp.html Phe, Tyr, Trp], [http://subtiwiki.uni-goettingen.de/pathways/folate_biosynthesis.html Folate]'''