DnaN - Revision history

Jstuelk at 11:27, 3 September 2015

2015-09-03T11:27:32Z

Jstuelk: /* Database entries */

2015-02-16T18:16:34Z

‎Database entries

Fabian Commichau: /* Biological materials */

2014-10-07T13:46:29Z

‎Biological materials

Jstuelk: /* Original publications */

2014-09-19T11:38:00Z

‎Original publications

134.76.70.252 at 09:52, 17 April 2014

2014-04-17T09:52:55Z

134.76.38.147 at 12:44, 2 April 2014

2014-04-02T12:44:35Z

134.76.70.252 at 15:24, 11 November 2013

2013-11-11T15:24:20Z

Jstuelk: /* References */

2013-09-13T17:25:29Z

‎References

Jstuelk at 16:46, 8 August 2013

2013-08-08T16:46:15Z

Jstuelk at 16:45, 8 August 2013

2013-08-08T16:45:21Z

← Older revision		Revision as of 11:27, 3 September 2015
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	{{#bank: DnaN}}		{{#bank: DnaN}}
−

← Older revision		Revision as of 18:16, 16 February 2015
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−	* '''Description:''' DNA polymerase III (beta subunit), beta clamp, part of the [[replisome]], also involved in DNA mismatch repair, inhibitor of [[DnaA]] oligomerization <br/><br/>	+	{{#bank: DnaN}}
−	{~~\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''dnaN''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''dnaG, dnaK ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]~~
−	\|-
−	~~\|style="background:~~#~~ABCDEF;" align="center"\| '''Product''' \|\| DNA polymerase III <br/>(beta subunit), beta clamp~~
−	\|-
−	~~\|style="background~~:~~#ABCDEF;" align="center"\|'''Function''' \|\| [[DNA replication]], DNA repair~~
−	\|-
−	\|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=BSU00020 DnaN]
−	\|-
−	\|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=DnaN DnaN]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 41 kDa, 4.718~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1134 bp, 378 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[dnaA]]'', ''[[yaaA]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00020 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00020 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00020 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:DnaA_dnaN_yaaA_recF_yaaB_gyrB_context.png]]~~
−	~~<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=dnaN_1939_3075_1 Expression at a glance]'''   {{PubMed\|22383849~~}~~}<br/>[[Image:DnaN_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00020]]~~
−	\|-
−	\|}

−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[DNA replication]]}},~~
−	~~{{SubtiWiki category\|[[essential genes]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[Spo0A regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU00020
−
−	~~===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=BSU00020&redirect=T BSU00020]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dnaAN.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10066]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** [[DnaN]] overexpression or release from the [[replisome]] decreases association of [[YabA]] with ''oriC'', increases association of [[DnaA]] with ''oriC'' {{PubMed\|21895792}}
−	** Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1) (according to Swiss-Prot)
−	** recruits [[MutS]] to the site of [[DNA replication]] ([[replisome]]) {{PubMed\|23228104}}
−	** required for bacteriophage SPP1 replication {{PubMed\|23268446}}
−	** inhibits oligomerization and helix formation of [[DnaA]] {{PubMed\|23909787}}
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[DnaA]]-[[YabA]]-[[DnaN]] {{PubMed\|12060778}}
−	** part of the [[replisome]]: [[PolC]]-[[HolA]]-[[HolB]]-[[DnaX]]-[[DnaN]]-[[DnaG]]-[[DnaC]]-[[DnaI]]-[[DnaD]]-[[SsbA]]-[[DnaE]]-[[PriA]]-[[DnaB]] {{PubMed\|20122408}}
−	** [[PolY1]]-[[DnaN]], [[PolY2]]-[[DnaN]] (required for untargeted mutagenesis) {{PubMed\|15469515}}
−	** [[PolY1]]-[[PolA]]-[[DnaN]] {{PubMed\|16045613}}
−	** [[MutL]] (C-terminal domain)-[[DnaN]] {{PubMed\|21050827}}
−	** [[MutS]]-[[DnaN]] {{PubMed\|20453097}}
−	** [[DnaE]]-[[DnaN]] {{PubMed\|21958350}}
−	** [[DnaN]] forms dimers {{PubMed\|16045613}}
−
−	* '''[[Localization]]:'''
−	** nucleoid (mid-cell spot) [http://www.ncbi.nlm.nih.gov/sites/entrez/9822387 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
−	** forms large assemblies on DNA, called "clamp zones" {{PubMed\|21419346}}
−	** forms foci {{PubMed\|21958350}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00020&redirect=T BSU00020]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P05649 P05649]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00020]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.7.7 2.7.7.7]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[dnaA]]-[[dnaN]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dnaN_1939_3075_1 dnaN] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|2987848}}
−
−	* '''Regulation:''' negatively controlled by [[DnaA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2168872 PubMed] and [[Spo0A]] [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
−	** repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 376 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 2265 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:''' [http://www.ncbi.nlm.nih.gov/sites/entrez/16942601 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/9822387 PubMed]
−
−	* '''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=~~
−	~~[[Philippe Noirot]], Jouy-en-Josas, France [http://locus.jouy.inra.fr/cms/index.php?id=18 homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed> 20157337 22933559 </pubmed>~~
−	~~== Original publications ==~~
−	<pubmed>16942601 9822387 14651647,2987848 2168872 14651647 12060778 16461910, 16479537 19737352 19081080 11395445 20122408 20451384 15469515 16045613 21895792 20453097 23228104 23268446,21050827,21419346,21958350 23909787 25170813 </pubmed>
−	~~[[Category:Protein-coding genes]]~~

@@ Line 147: / Line 147: @@
 * '''GFP fusion:'''  [http://www.ncbi.nlm.nih.gov/sites/entrez/16942601 PubMed]  [http://www.ncbi.nlm.nih.gov/sites/entrez/9822387 PubMed]
-* '''two-hybrid system:'''
+* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Fabian Commichau]]'s lab
 * '''Antibody:'''

@@ Line 160: / Line 160: @@
 <pubmed> 20157337 22933559 </pubmed>
 == Original publications ==
-<pubmed>16942601 9822387 14651647,2987848 2168872 14651647 12060778 16461910, 16479537 19737352 19081080 11395445 20122408 20451384 15469515 16045613 21895792 20453097 23228104 23268446,21050827,21419346,21958350 23909787 </pubmed>
+<pubmed>16942601 9822387 14651647,2987848 2168872 14651647 12060778 16461910, 16479537 19737352 19081080 11395445 20122408 20451384 15469515 16045613 21895792 20453097 23228104 23268446,21050827,21419346,21958350 23909787 25170813 </pubmed>
 [[Category:Protein-coding genes]]

← Older revision		Revision as of 09:52, 17 April 2014
Line 134:		Line 134:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 376 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 2265 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 56: / Line 56: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dnaAN.html]
@@ Line 106: / Line 107: @@
 === Database entries ===
 * '''Structure:'''

@@ 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=BSU00020 DnaN]
 |-
-|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/DnaN DnaN]
+|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=DnaN DnaN]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 4.718

@@ Line 154: / Line 154: @@
 =References=
 ==Reviews==
-<pubmed> 20157337 </pubmed>
+<pubmed> 20157337 22933559 </pubmed>
-==Original publications==
+== Original publications ==
 <pubmed>16942601 9822387 14651647,2987848 2168872 14651647 12060778 16461910, 16479537 19737352 19081080 11395445 20122408 20451384 15469515 16045613 21895792 20453097 23228104 23268446,21050827,21419346,21958350 23909787 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 1: / Line 1: @@
-* '''Description:''' DNA polymerase  III (beta subunit), beta clamp, part of the [[replisome]], also involved in DNA mismatch repair <br/><br/>
+* '''Description:''' DNA polymerase  III (beta subunit), beta clamp, part of the [[replisome]], also involved in DNA mismatch repair, inhibitor of [[DnaA]] oligomerization <br/><br/>
 {| align="right" border="1" cellpadding="2"
 |-
@@ Line 72: / Line 72: @@
 ** recruits [[MutS]] to the site of [[DNA replication]] ([[replisome]]) {{PubMed|23228104}}
 ** required for bacteriophage SPP1 replication {{PubMed|23268446}}
-** inhibits oligomerization of [[DnaA]] {{PubMed|23909787}}
+** inhibits oligomerization and helix formation of [[DnaA]] {{PubMed|23909787}}
 * '''Protein family:'''