PcrA - Revision history

Jstuelk: /* Original Publications */

2015-06-15T05:54:44Z

‎Original Publications

Fabian Commichau: /* Biological materials */

2014-10-07T13:45:05Z

‎Biological materials

134.76.70.252 at 09:36, 17 April 2014

2014-04-17T09:36:43Z

134.76.38.147 at 13:08, 2 April 2014

2014-04-02T13:08:35Z

Jstuelk at 18:42, 17 November 2013

2013-11-17T18:42:31Z

Jstuelk at 18:34, 17 November 2013

2013-11-17T18:34:35Z

134.76.70.252 at 15:20, 11 November 2013

2013-11-11T15:20:39Z

134.76.70.252 at 12:43, 16 May 2013

2013-05-16T12:43:02Z

134.76.70.252 at 09:38, 14 May 2013

2013-05-14T09:38:21Z

134.76.70.252 at 12:17, 13 May 2013

2013-05-13T12:17:59Z

← Older revision		Revision as of 05:54, 15 June 2015
Line 1:		Line 1:
−	* '''Description:''' ATP-dependent DNA helicase, facilitates unwinding of ICEBs1 DNA for horizontal transfer <br/><br/>	+	{{#bank: PcrA}}
−	{~~\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''pcrA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yerF ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| ATP-dependent DNA helicase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| plasmid rolling-circle replication, conjugative transfer of ICEBs1~~
−	\|-
−	~~\|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=BSU06610 pcrA]~~
−	\|-
−	\|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=PcrA PcrA]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 83 kDa, 5.767~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 2217 bp, 739 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[pcrB]]'', ''[[ligA]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU06610 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU06610 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU06610 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:pcrA_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=pcrA_719370_721589_1 Expression at a glance]'''   {{PubMed\|22383849~~}~~}<br/>[[Image:pcrA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU06610]]~~
−	\|-
−	\|}

−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[DNA repair/ recombination]]}},~~
−	~~{{SubtiWiki category\|[[mobile genetic elements]]}},~~
−	~~{{SubtiWiki category\|[[essential genes]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[LexA regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU06610
−
−	~~===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=BSU06610&redirect=T BSU06610]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pcrBA-ligA-yerH.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12834]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** PcrA anchors itself to the template duplex using the 2B subdomain and reels in the lagging strand, extruding a single-stranded loop {{PubMed\|20723756}}
−	** dismantles [[RecA]] filaments {{PubMed\|20723756}}
−
−	* '''Protein family:''' uvrD-like helicase C-terminal domain (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):''' [[YjcD]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−	** two RecA-like domains {{PubMed\|24147116}}
−	** intrinxically disordered C-terminal domain (for interaction with [[RNA polymerase]]) {{PubMed\|24147116}}
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−	** unwinding of the double-stranded ICEBs1 DNA is stimulated by [[HelP]] {{PubMed\|23326247}}
−	** helicase activity is stimulated by interaction with [[RNA polymerase]] {{PubMed\|24147116}}
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** the C-terminal domain of [[PcrA]] interacts with the [[RNA polymerase]] {{PubMed\|24147116,21710567}}
−	** [[YxaL]]-[[PcrA]] {{PubMed\|12073041}}
−	** [[YerB]]-[[PcrA]] {{PubMed\|12073041}}
−	** [[YwhK]]-[[PcrA]] {{PubMed\|12073041}}
−	** [[UvrB]]-[[PcrA]] {{PubMed\|24147116}}
−	** [[YwqA]]-[[PcrA]] {{PubMed\|24147116}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU06610&redirect=T BSU06610]
−
−	* '''Structure:'''
−	** [http://www.rcsb.org/pdb/explore.do?structureId=2PJR 2PJR] (product complex, complex with sulphate ion, ''Geobacillus stearothermophilus'')
−	** [http://www.rcsb.org/pdb/explore.do?structureId=1PJR 1PJR] (substrate complex, complex with DNA, ''Geobacillus stearothermophilus'')
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O34580 O34580]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU06610]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[pcrB]]-[[pcrA]]-[[ligA]]-[[yerH]]'' {{PubMed\|9701819}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pcrA_719370_721589_1 pcrA] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−	** induced by DNA damage ([[LexA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16267290 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[LexA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16267290 PubMed]
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 114 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 250 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Fabian Commichau]]'s lab
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed> 19943906 </pubmed>~~
−	~~==Original Publications==~~
−	~~<pubmed>12073041,9701819 ,16267290, 19943900 20723756 18276648 17449621 10899133 10199404 23326247 24147116 21710567</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 146: / Line 146: @@
 * '''GFP fusion:'''
-* '''two-hybrid system:'''
+* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Fabian Commichau]]'s lab
 * '''Antibody:'''

← Older revision		Revision as of 09:36, 17 April 2014
Line 133:		Line 133:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 114 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 250 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 57: / Line 57: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pcrBA-ligA-yerH.html]
@@ Line 103: / Line 104: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 81: / Line 81: @@
 * '''Domains:'''
 * '''Modification:'''
@@ Line 88: / Line 90: @@
 * '''Effectors of protein activity:'''
 ** unwinding of the double-stranded ICEBs1 DNA is stimulated by [[HelP]] {{PubMed|23326247}}
 * '''[[SubtInteract|Interactions]]:'''
-** [[PcrA]] interacts with the [[RNA polymerase]] {{PubMed|21710567}}
+** the C-terminal domain of [[PcrA]] interacts with the [[RNA polymerase]] {{PubMed|24147116,21710567}}
 ** [[YxaL]]-[[PcrA]] {{PubMed|12073041}}
 ** [[YerB]]-[[PcrA]] {{PubMed|12073041}}
 ** [[YwhK]]-[[PcrA]] {{PubMed|12073041}}
 * '''[[Localization]]:'''
@@ Line 148: / Line 154: @@
 <pubmed> 19943906 </pubmed>
 ==Original Publications==
-'''Additional publications:''' {{PubMed|21710567}}
+<pubmed>12073041,9701819 ,16267290, 19943900 20723756 18276648 17449621 10899133 10199404 23326247 24147116 21710567</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 15: / Line 15: @@
 |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=BSU06610 pcrA]
 |-
-|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/PcrA PcrA]
+|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=PcrA PcrA]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 83 kDa, 5.767

@@ 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=pcrA_719370_721589_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:pcrA_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pcrA_719370_721589_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:pcrA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU06610]]
 |-
 |}

@@ Line 23: / Line 23: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pcrB]]'', ''[[ligA]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU06610 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU06610 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU06610 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU06610 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU06610 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU06610 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:pcrA_context.gif]]