TyrS - Revision history

Jstuelk at 15:16, 3 July 2015

2015-07-03T15:16:27Z

Jstuelk: /* Original publications */

2015-03-04T13:39:06Z

‎Original publications

Jstuelk at 13:11, 4 March 2015

2015-03-04T13:11:32Z

134.76.70.252 at 14:16, 17 April 2014

2014-04-17T14:16:20Z

134.76.70.252 at 09:48, 17 April 2014

2014-04-17T09:48:51Z

134.76.38.147 at 14:31, 2 April 2014

2014-04-02T14:31:37Z

Jstuelk at 16:41, 5 March 2014

2014-03-05T16:41:04Z

134.76.70.252 at 11:28, 7 January 2014

2014-01-07T11:28:13Z

Jstuelk at 14:34, 12 July 2013

2013-07-12T14:34:04Z

134.76.70.252 at 14:19, 16 May 2013

2013-05-16T14:19:13Z

← Older revision		Revision as of 15:16, 3 July 2015
Line 1:		Line 1:
−	* '''Description:~~''' tyrosyl-tRNA synthetase (major) <br/><br/>~~	+	{{#bank: TyrS}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''tyrS''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| tyrosyl-tRNA synthetase (major)~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| translation~~
−	\|-
−	\|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=BSU29670 tyrS]
−	\|-
−	\|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=tyrS tyrS]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 47 kDa, 5.213~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1266 bp, 422 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[rpsD]]'', ''[[ytzK]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29670 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29670 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29670 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:tyrS_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=tyrS_3036603_3037871_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:tyrS_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29670]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[translation]]}},~~
−	~~{{SubtiWiki category\|[[essential genes]]}},~~
−	~~[[most abundant proteins]]~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[T-box]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU29670
−
−	~~===Phenotypes of a mutant ===~~
−	* essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
−	* the gene can be deleted, but the mutant acquires suppressors in ''[[dtrR]]'' to allow expression of ''[[tyrZ]]'' {{PubMed\|25733610}}
−	* a ''[[tyrS]] [[tyrZ]]'' double mutant is not viable {{PubMed\|25733610}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU29670&redirect=T BSU29670]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/tyrS.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10371]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU29670&redirect=T BSU29670]
−
−	* '''Structure:'''
−	** [http://www.rcsb.org/pdb/explore.do?structureId=1JH3 1JH3] (C-terminal domain, Geobacillus stearothermophilus)
−	** [http://www.rcsb.org/pdb/explore.do?structureId=3TS1 3TS1] (complex with tyrosyl adenylate intermediate, Geobacillus stearothermophilus)
−	** [http://www.rcsb.org/pdb/explore.do?structureId=1N53 1N53] (the [[T-box]] antiterminator RNA) [http://www.ncbi.nlm.nih.gov/sites/entrez/12547201 PubMed]
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P22326 P22326]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29670]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[tyrS]]'' {{PubMed\|1735721}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tyrS_3036603_3037871_-1 tyrS] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|1735721}}
−
−	* '''Regulation:'''
−	** induced by tyrosine limitation ([[T-box]]) {{PubMed\|19258532}}
−
−	* '''Regulatory mechanism:'''
−	** [[T-box]]: [[RNA switch]], transcriptional antitermination {{PubMed\|19258532}}
−
−	* '''Additional information:'''
−	** belongs to the 100 [[most abundant proteins]] {{PubMed\|15378759}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 848 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 3406 {{PubMed\|24696501}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 4314 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 1369 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 1521 {{PubMed\|21395229}}
−
−	~~=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>19258532,10546897 </pubmed>~~
−	~~==Original publications==~~
−	~~<pubmed>9098057,12547201,11842119,10943892,9282752,8045882,8348614,1735721,8289305,20110252 , 21333656 15378759 25733610 25733611</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 152: / Line 152: @@
 <pubmed>19258532,10546897 </pubmed>
 ==Original publications==
-<pubmed>9098057,12547201,11842119,10943892,9282752,8045882,8348614,1735721,8289305,20110252 , 21333656 15378759 25733610</pubmed>
+<pubmed>9098057,12547201,11842119,10943892,9282752,8045882,8348614,1735721,8289305,20110252 , 21333656 15378759 25733610 25733611</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 54: / Line 54: @@
 ===Phenotypes of a mutant ===
+* essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
-essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+* the gene can be deleted, but the mutant acquires suppressors in ''[[dtrR]]'' to allow expression of ''[[tyrZ]]'' {{PubMed|25733610}}
 === Database entries ===
@@ Line 151: / Line 152: @@
 <pubmed>19258532,10546897 </pubmed>
 ==Original publications==
-<pubmed>9098057,12547201,11842119,10943892,9282752,8045882,8348614,1735721,8289305,20110252 , 21333656 15378759</pubmed>
+<pubmed>9098057,12547201,11842119,10943892,9282752,8045882,8348614,1735721,8289305,20110252 , 21333656 15378759 25733610</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 126: / Line 126: @@
 ** number of protein molecules per cell (minimal medium with glucose and ammonium): 848 {{PubMed|24696501}}
 ** number of protein molecules per cell (complex medium with amino acids, without glucose): 3406 {{PubMed|24696501}}
 =Biological materials =
 * '''Mutant:'''

@@ Line 124: / Line 124: @@
 * '''Additional information:'''
 ** belongs to the 100 [[most abundant proteins]] {{PubMed|15378759}}
 =Biological materials =

@@ Line 58: / Line 58: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/tyrS.html]
@@ Line 92: / Line 93: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 41: / Line 41: @@
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[translation]]}},
-{{SubtiWiki category|[[essential genes]]}}
+{{SubtiWiki category|[[essential genes]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 63: / Line 64: @@
 === Additional information===
 =The protein=
@@ Line 81: / Line 79: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 114: / Line 112: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tyrS_3036603_3037871_-1 tyrS] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] {{PubMed|1735721}}
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|1735721}}
 * '''Regulation:'''
@@ Line 123: / Line 121: @@
 * '''Additional information:'''
 =Biological materials =
@@ Line 146: / Line 145: @@
 <pubmed>19258532,10546897 </pubmed>
 ==Original publications==
-<pubmed>9098057,12547201,11842119,10943892,9282752,8045882,8348614,1735721,8289305,20110252 , 21333656 </pubmed>
+<pubmed>9098057,12547201,11842119,10943892,9282752,8045882,8348614,1735721,8289305,20110252 , 21333656 15378759</pubmed>
 [[Category:Protein-coding genes]]

@@ 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=BSU29670 tyrS]
 |-
-|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/tRNA_charging.html tRNA charging]'''
+|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=tyrS tyrS]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 5.213

@@ Line 37: / Line 37: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 99: / Line 95: @@
 === Database entries ===
-* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1N53 1N53] (the [[T-box]] antiterminator RNA) [http://www.ncbi.nlm.nih.gov/sites/entrez/12547201 PubMed], [http://www.rcsb.org/pdb/explore.do?structureId=1JH3 1JH3] (C-terminal domain, Geobacillus stearothermophilus),  [http://www.rcsb.org/pdb/explore.do?structureId=3TS1 3TS1] (complex with tyrosyl adenylate intermediate,  Geobacillus stearothermophilus)
+* '''Structure:'''
 * '''UniProt:''' [http://www.uniprot.org/uniprot/P22326 P22326]

@@ Line 29: / Line 29: @@
   <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=tyrS_3036603_3037871_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:tyrS_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tyrS_3036603_3037871_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:tyrS_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29670]]
 |-
 |}