YrvO - Revision history

Jstuelk at 12:25, 1 April 2015

2015-04-01T12:25:35Z

Jstuelk: /* Basic information/ Evolution */

2015-04-01T12:08:52Z

‎Basic information/ Evolution

Jstuelk at 12:06, 1 April 2015

2015-04-01T12:06:52Z

Jstuelk at 12:06, 1 April 2015

2015-04-01T12:06:30Z

134.76.70.252 at 09:38, 17 April 2014

2014-04-17T09:38:53Z

134.76.38.147 at 14:22, 2 April 2014

2014-04-02T14:22:18Z

134.76.70.252 at 14:05, 16 May 2013

2013-05-16T14:05:47Z

134.76.70.252 at 13:27, 13 May 2013

2013-05-13T13:27:05Z

134.76.70.252 at 14:22, 7 August 2012

2012-08-07T14:22:16Z

Jstuelk at 18:12, 21 April 2012

2012-04-21T18:12:58Z

← Older revision		Revision as of 12:25, 1 April 2015
Line 1:		Line 1:
−	* '''Description:~~''' cysteine desulfurase involved in 2-thiouridine (s2U) modification of the wobble position in glutamate, glutamine and lysine tRNA molecules<br/><br/>~~	+	{{#bank: YrvO}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''yrvO''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''nifS, iscS''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| cysteine desulfurase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| tRNA modification~~
−	\|-
−	\|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=BSU27510 yrvO]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 41 kDa, 5.463~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1137 bp, 379 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[trmU]]'', ''[[cymR]]''~~
−	\|-
−	~~\|style="background:#FAF8CC;" align="center"\|'''[http://subtiwiki.uni-goettingen.de/yrvO_nucleotide.txt Gene sequence (+200bp) ]'''~~
−	~~\|style="background:#FAF8CC;" align="center"\|'''[http://subtiwiki.uni-goettingen.de/yrvO_protein.txt Protein sequence]'''~~
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yrvO_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=iscS_2810559_2811698_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:yrvO_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU27510]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[essential genes]]}},~~
−	~~{{SubtiWiki category\|[[translation]]}},~~
−	~~{{SubtiWiki category\|[[phosphoproteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[stringent response]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU27510
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU27510&redirect=T BSU27510]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cymR-yrvO-trmU.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13809]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** 2-thiouridine (s2U) modification of the wobble position in glutamate, glutamine and lysine tRNA molecules (together with [[TrmU]]) {{PubMed\|25825430}}
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):''' [[NifS]], [[NifZ]], [[SufS]], [[YcbU]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−	** phosphorylated on Arg-385 {{PubMed\|22517742}}
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU27510&redirect=T BSU27510]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=1EG5 1EG5] (from Thermotoga maritima, 37% identity, 54% similarity) {{PubMed\|10715213}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O34599 O34599]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU27510]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:''' ''[[cymR]]-[[yrvO]]-[[trmU]]'' {{PubMed\|16885442}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=iscS_2810559_2811698_-1 yrvO] {{PubMed\|22383849}}
−
−	* '''Sigma factor:''' [[SigA]] {{PubMed\|16885442}}
−
−	* '''Regulation:'''
−	** [[RelA]] dependent downregulation (Class I) during stringent response {{PubMed\|11948165}}
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 184 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 444 {{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=~~
−	~~<pubmed>16885442 11948165 10715213 22517742 12682299 17064282 25825430</pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

@@ Line 70: / Line 70: @@
 * '''Catalyzed reaction/ biological activity:'''
-** 2-thiouridine (s2U) modification of the wobble position in glutamate, glutamine and lysine tRNA molecules (together with [[MnmA]]) {{PubMed|25825430}}
+** 2-thiouridine (s2U) modification of the wobble position in glutamate, glutamine and lysine tRNA molecules (together with [[TrmU]]) {{PubMed|25825430}}
 * '''Protein family:'''

← Older revision		Revision as of 12:06, 1 April 2015
Line 1:		Line 1:
−	* '''Description:''' cysteine desulfurase involved 2-thiouridine (s2U) modification of the wobble position in glutamate, glutamine and lysine tRNA molecules<br/><br/>	+	* '''Description:''' cysteine desulfurase involved in 2-thiouridine (s2U) modification of the wobble position in glutamate, glutamine and lysine tRNA molecules<br/><br/>

	{\| align="right" border="1" cellpadding="2"		{\| align="right" border="1" cellpadding="2"

@@ Line 1: / Line 1: @@
-* '''Description:'''  cysteine desulfurase involved in tRNA thiolation<br/><br/>
+* '''Description:'''  cysteine desulfurase involved 2-thiouridine (s2U) modification of the wobble position in glutamate, glutamine and lysine tRNA molecules<br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 36: / Line 36: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
@@ Line 74: / Line 70: @@
 * '''Catalyzed reaction/ biological activity:'''
 * '''Protein family:'''
@@ Line 144: / Line 141: @@
 =References=
-<pubmed>16885442 11948165 10715213 22517742 12682299 17064282</pubmed>
+<pubmed>16885442 11948165 10715213 22517742 12682299 17064282 25825430</pubmed>
 [[Category:Protein-coding genes]]

← Older revision		Revision as of 09:38, 17 April 2014
Line 122:		Line 122:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 184 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 444 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 61: / Line 61: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cymR-yrvO-trmU.html]
@@ Line 96: / Line 97: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=1EG5 1EG5] (from Thermotoga maritima, 37% identity, 54% similarity) {{PubMed|10715213}}

@@ Line 28: / Line 28: @@
   <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=iscS_2810559_2811698_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yrvO_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=iscS_2810559_2811698_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yrvO_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU27510]]
 |-
 |}

@@ Line 14: / Line 14: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || tRNA modification
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU27510 yrvO]
+|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=BSU27510 yrvO]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.463

@@ Line 1: / Line 1: @@
-* '''Description:''' cysteine desulfurase<br/><br/>
+* '''Description:'''  cysteine desulfurase involved in tRNA thiolation<br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 12: / Line 12: @@
 |style="background:#ABCDEF;" align="center"| '''Product''' || cysteine desulfurase
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+|style="background:#ABCDEF;" align="center"|'''Function''' || tRNA modification
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.463
@@ Line 42: / Line 42: @@
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[essential genes]]}},
-{{SubtiWiki category|[[poorly characterized/ putative enzymes]]}},
+{{SubtiWiki category|[[translation]]}},
 {{SubtiWiki category|[[phosphoproteins]]}}
@@ Line 138: / Line 138: @@
 =References=
-<pubmed>16885442 11948165 10715213 22517742</pubmed>
+<pubmed>16885442 11948165 10715213 22517742 12682299 17064282</pubmed>
 [[Category:Protein-coding genes]]