CopA - Revision history

134.76.70.252 at 11:53, 8 April 2014

2014-04-08T11:53:13Z

134.76.38.147 at 14:45, 2 April 2014

2014-04-02T14:45:27Z

Jstuelk: /* Database entries */

2014-01-08T13:34:50Z

‎Database entries

Jstuelk at 13:33, 8 January 2014

2014-01-08T13:33:15Z

134.76.70.252 at 14:21, 18 November 2013

2013-11-18T14:21:03Z

134.76.70.252 at 14:34, 16 May 2013

2013-05-16T14:34:31Z

134.76.70.252 at 11:16, 14 May 2013

2013-05-14T11:16:10Z

134.76.70.252 at 13:50, 13 May 2013

2013-05-13T13:50:54Z

Jstuelk: /* Reviews */

2012-10-14T18:15:00Z

‎Reviews

134.76.70.252 at 15:55, 7 August 2012

2012-08-07T15:55:57Z

← Older revision		Revision as of 11:53, 8 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' copper-transporting ATPase, resistance to copper <br/><br/>~~	+	{{#bank: CopA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''copA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yvgX ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| copper transporting ATPase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| copper export, detoxification~~
−	\|-
−	\|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=BSU33500 copA]
−	\|-
−	\|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=CopA CopA]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Metabolic function and regulation of this protein in [[SubtiPathways\|''Subti''Pathways]]: <br/>[http://cellpublisher.gobics.de/view/GqbblRJkBH metal ion homeostasis]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 85 kDa, 5.484~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 2409 bp, 803 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[cadA]]'', ''[[copZ]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU33500 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU33500 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU33500 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yvgX_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=copA_3441121_3443529_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:copA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU33500]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[transporters/ other]]}},~~
−	~~{{SubtiWiki category\|[[trace metal homeostasis (Cu, Zn, Ni, Mn, Mo)]]}},~~
−	~~{{SubtiWiki category\|[[resistance against toxic metals]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CsoR regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU33500
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU33500&redirect=T BSU33500]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14106]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' ATP + H<sub>2</sub>O + Cu<sup>1+</sup>(In) = ADP + phosphate + Cu<sup>1+</sup>(Out) (according to Swiss-Prot)
−
−	* '''Protein family:''' Type IB subfamily (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−	** two N-terminal soluble domains, CopAa and CopAb, connected by a short linker
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[CopA]]-[[CopZ]], for the transfer of the Cu(I) cluster {{PubMed\|19751213}}
−
−	* '''[[Localization]]:''' cell membrane (according to Swiss-Prot)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU33500&redirect=T BSU33500]
−
−	* '''Structure:'''
−	** [http://www.rcsb.org/pdb/explore.do?structureId=2RML 2RML] ( N-terminal soluble domain)
−	** [http://www.pdb.org/pdb/explore/explore.do?structureId=4BBJ 4BBJ] (the protein from ''Legionella pneumophila'', 45% identity, 79% similarity) {{PubMed\|24317491}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O32220 O32220]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33500]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:''' ''[[copZ]]-[[copA]]'' {{PubMed\|12779235}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=copA_3441121_3443529_-1 copA] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|12779235}}
−
−	* '''Regulation:'''
−	** induced by copper ([[CsoR]]) {{PubMed\|18048925,12779235}}
−
−	* '''Regulatory mechanism:'''
−	** [[CsoR]]: transcription repression {{PubMed\|18048925}}
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−	~~[[John Helmann]], Cornell University, USA [http://www.micro.cornell.edu/research/labs/helmann-lab/index.cfm Homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>19824702 23046649</pubmed>~~
−
−	~~==Original publications==~~
−	~~<pubmed>19751213 11922674,12590580,14663075,12779235,12644235,18048925,14514665,14711369, 19378562 15212800 20233928 24317491 22531974,22077885</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 59: / Line 59: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 95: / Line 96: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 98: / Line 98: @@
 * '''Structure:'''
 ** [http://www.rcsb.org/pdb/explore.do?structureId=2RML 2RML] ( N-terminal soluble domain)
-** [http://www.pdb.org/pdb/explore/explore.do?structureId=4BBJ 4BBJ] (the protein from Legionella pneumophila, 45% identity, 79% similarity) {{PubMed|24317491}}
+** [http://www.pdb.org/pdb/explore/explore.do?structureId=4BBJ 4BBJ] (the protein from ''Legionella pneumophila'', 45% identity, 79% similarity) {{PubMed|24317491}}
 * '''UniProt:''' [http://www.uniprot.org/uniprot/O32220 O32220]

@@ Line 39: / Line 39: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
@@ Line 69: / Line 65: @@
 === Additional information===
 =The protein=
@@ Line 87: / Line 80: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 ** two N-terminal soluble domains, CopAa and CopAb, connected by a short linker
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 103: / Line 96: @@
 === Database entries ===
-* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2RML 2RML] ( N-terminal soluble domain)
+* '''Structure:'''
 * '''UniProt:''' [http://www.uniprot.org/uniprot/O32220 O32220]
@@ Line 118: / Line 113: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=copA_3441121_3443529_-1 copA] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] {{PubMed|12779235}}
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|12779235}}
 * '''Regulation:'''
 ** induced by copper ([[CsoR]]) {{PubMed|18048925,12779235}}
@@ Line 151: / Line 147: @@
 ==Original publications==
-'''Additional publications:''' {{PubMed|22531974,22077885}}
+<pubmed>19751213 11922674,12590580,14663075,12779235,12644235,18048925,14514665,14711369, 19378562 15212800  20233928 24317491 22531974,22077885</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=BSU33500 copA]
 |-
-|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/CopA CopA]
+|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=CopA CopA]
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://cellpublisher.gobics.de/view/GqbblRJkBH metal ion homeostasis]'''

@@ 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=copA_3441121_3443529_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:copA_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=copA_3441121_3443529_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:copA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU33500]]
 |-
 |}

@@ Line 26: / Line 26: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cadA]]'', ''[[copZ]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU33500 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU33500 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU33500 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU33500 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU33500 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU33500 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yvgX_context.gif]]

@@ Line 148: / Line 148: @@
 =References=
 ==Reviews==
-<pubmed> 19824702 </pubmed>
+<pubmed>19824702 23046649</pubmed>
 ==Original publications==
 '''Additional publications:''' {{PubMed|22531974,22077885}}

@@ Line 13: / Line 13: @@
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || copper export, detoxification
 |-
 |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/CopA CopA]