AddB - Revision history

Jstuelk: /* Original publications */

2015-08-10T11:16:46Z

‎Original publications

Jstuelk at 08:03, 7 July 2015

2015-07-07T08:03:54Z

Jstuelk at 09:15, 7 May 2015

2015-05-07T09:15:17Z

Jstuelk at 11:31, 11 December 2014

2014-12-11T11:31:53Z

Jstuelk: /* Reviews */

2014-06-26T13:06:44Z

‎Reviews

Jstuelk: /* Original publications */

2014-06-26T13:02:49Z

‎Original publications

134.76.38.147 at 13:22, 2 April 2014

2014-04-02T13:22:02Z

Jstuelk at 10:42, 2 April 2014

2014-04-02T10:42:23Z

134.76.70.252 at 15:57, 11 November 2013

2013-11-11T15:57:48Z

Jstuelk: /* References */

2013-09-13T15:37:42Z

‎References

← Older revision		Revision as of 11:16, 10 August 2015
Line 1:		Line 1:
−	* '''Description:''' ATP-dependent deoxyribonuclease (subunit B), required for efficient survival and replication restart after replication-transcription conflicts <br/><br/>	+	{{#bank: AddB}}
−	{~~\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''addB''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| ATP-dependent deoxyribonuclease (subunit B))~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| [[DNA repair/ recombination]]~~
−	\|-
−	~~\|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=BSU10620 addB]~~
−	\|-
−	\|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=AddB ~~AddB]~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 134 kDa, 5.39~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 3498 bp, 1166 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yhjR]]'', ''[[addA]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU10620 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU10620 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU10620 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:addB_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=addB_1136320_1139820_1 Expression at a glance]'''   {{PubMed\|22383849~~}~~}<br/>[[Image:addB_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU10620]]~~
−	\|-
−	\|}

−	~~__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\|[[genetic competence]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[ComK regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU10620
−
−	~~===Phenotypes of a mutant ===~~
−	* ''[[recO]] [[addA]]-[[addB]]'' double mutants are extremely sensitive against DNA damaging agents {{PubMed\|26001966}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU10620&redirect=T BSU10620]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/addBA.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10465]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** the enzyme is functional as a heterodimer of the [[AddA]] and [[AddB]] subunits, that it is a rapid and processive DNA helicase, and that it catalyses DNA unwinding using one single-stranded DNA motor of 3'→5' polarity located in the [[AddA]] subunit {{PubMed\|21071401}}
−	** the [[AddB]] subunit contains a second putative ATP-binding pocket, but this does not contribute to the observed helicase activity and may instead be involved in the recognition of recombination hotspot sequences {{PubMed\|21071401}}
−
−	* '''Protein family:''' uvrD-like helicase C-terminal domain (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[AddA]]-[[AddB]] {{PubMed\|10756102,21071401}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU10620&redirect=T BSU10620]
−
−	* '''Structure:'''
−	** [http://www.rcsb.org/pdb/explore/explore.do?structureId=3U4Q 3U4Q] (the [[AddA]]-[[AddB]]-DNA complex) {{PubMed\|22307084}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P23477 P23477]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU10620]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[addB]]-[[addA]]-[[sbcD]]-[[sbcC]]-[[hlpB]]'' {{PubMed\|22383849}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=addB_1136320_1139820_1 addB] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|7746142}}
−
−	* '''Regulation:'''
−	** positive control by [[ComK]] {{PubMed\|7746142}}
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:''' GP1106 ([[addA]]-[[addB]], spc), available in [[Jörg Stülke]]'s lab
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−	* [[Mark Dillingham]], Bristol, U.K. ([http://www.bris.ac.uk/biochemistry/research/md.html homepage])
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed> 23202527, 20116346 22933559 19542287 25486468 </pubmed>~~
−	~~==Original publications==~~
−	~~<pubmed>21809208,8387145,15610857,7746142, 19129187 1646786 10756102 9781875 17570399 20350930 22307084 22383849 21071401 23056615 24682829 24670664 8752329 25939832 26001966</pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

@@ Line 54: / Line 54: @@
 ===Phenotypes of a mutant ===
 === Database entries ===
@@ Line 145: / Line 146: @@
 <pubmed> 23202527, 20116346 22933559 19542287 25486468 </pubmed>
 ==Original publications==
-<pubmed>21809208,8387145,15610857,7746142, 19129187 1646786 10756102 9781875 17570399 20350930 22307084 22383849 21071401 23056615 24682829 24670664 8752329 25939832</pubmed>
+<pubmed>21809208,8387145,15610857,7746142, 19129187 1646786 10756102 9781875 17570399 20350930 22307084 22383849 21071401 23056615 24682829 24670664 8752329 25939832 26001966</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 1: / Line 1: @@
-* '''Description:''' ATP-dependent deoxyribonuclease (subunit B) <br/><br/>
+* '''Description:''' ATP-dependent deoxyribonuclease (subunit B), required for efficient survival and replication restart after replication-transcription conflicts <br/><br/>
 {| align="right" border="1" cellpadding="2"
 |-
@@ Line 145: / Line 145: @@
 <pubmed> 23202527, 20116346 22933559 19542287 25486468 </pubmed>
 ==Original publications==
-<pubmed>21809208,8387145,15610857,7746142, 19129187 1646786 10756102 9781875 17570399 20350930 22307084 22383849 21071401 23056615 24682829 24670664 8752329 </pubmed>
+<pubmed>21809208,8387145,15610857,7746142, 19129187 1646786 10756102 9781875 17570399 20350930 22307084 22383849 21071401 23056615 24682829 24670664 8752329 25939832</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 124: / Line 124: @@
 =Biological materials =
-* '''Mutant:''' GP1106 (addAB, spc), available in [[Stülke]] lab
+* '''Mutant:''' GP1106 ([[addA]]-[[addB]], spc), available in [[Jörg Stülke]]'s lab
 * '''Expression vector:'''
@@ Line 143: / Line 143: @@
 =References=
 ==Reviews==
-<pubmed> 23202527, 20116346 22933559 19542287 </pubmed>
+<pubmed> 23202527, 20116346 22933559 19542287 25486468 </pubmed>
 ==Original publications==
 <pubmed>21809208,8387145,15610857,7746142, 19129187 1646786 10756102 9781875 17570399 20350930 22307084 22383849 21071401 23056615 24682829 24670664 8752329 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 143: / Line 143: @@
 =References=
 ==Reviews==
-<pubmed> 23202527, 20116346 22933559</pubmed>
+<pubmed> 23202527, 20116346 22933559 19542287 </pubmed>
 ==Original publications==
 <pubmed>21809208,8387145,15610857,7746142, 19129187 1646786 10756102 9781875 17570399 20350930 22307084 22383849 21071401 23056615 24682829 24670664 8752329 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 56: / Line 56: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/addBA.html]
@@ Line 93: / Line 94: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 38: / Line 38: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 62: / Line 62: @@
 === Additional information===
 =The protein=
@@ Line 81: / Line 79: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 113: / Line 111: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=addB_1136320_1139820_1 addB] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] {{PubMed|7746142}}
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|7746142}}
 * '''Regulation:'''
@@ Line 145: / Line 143: @@
 <pubmed> 23202527, 20116346 22933559</pubmed>
 ==Original publications==
-<pubmed>21809208,8387145,15610857,7746142, 19129187 1646786 10756102 9781875 17570399 20350930 22307084 22383849 21071401 23056615</pubmed>
+<pubmed>21809208,8387145,15610857,7746142, 19129187 1646786 10756102 9781875 17570399 20350930 22307084 22383849 21071401 23056615 24682829 24670664</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=BSU10620 addB]
 |-
-|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/AddB AddB]
+|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=AddB AddB]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 134 kDa, 5.39