Revision as of 14:26, 11 November 2013

Description: DNA polymerase III (beta subunit), beta clamp, part of the replisome, also involved in DNA mismatch repair, inhibitor of DnaA oligomerization

Gene name	dnaN
Synonyms	dnaG, dnaK
Essential	yes PubMed
Product	DNA polymerase III (beta subunit), beta clamp
Function	DNA replication, DNA repair
*Gene expression levels in SubtiExpress*: DnaN
*Interactions involving this protein in SubtInteract*: DnaN
MW, pI	41 kDa, 4.718
Gene length, protein length	1134 bp, 378 aa
Immediate neighbours	dnaA, yaaA
Sequences	Protein DNA DNA_with_flanks
Genetic context This image was kindly provided by SubtiList
Expression at a glance PubMed

Categories containing this gene/protein

DNA replication, essential genes

This gene is a member of the following regulons

Spo0A regulon

The gene

Basic information

Locus tag: BSU00020

Phenotypes of a mutant

essential PubMed

Database entries

DBTBS entry: [1]

SubtiList entry: [2]

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
- Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1) (according to Swiss-Prot)
- recruits MutS to the site of DNA replication (replisome) PubMed
- required for bacteriophage SPP1 replication PubMed
- inhibits oligomerization and helix formation of DnaA PubMed

Protein family:

Paralogous protein(s):

Extended information on the protein

Kinetic information:

Domains:

Modification:

Cofactor(s):

Effectors of protein activity:

Interactions:
- DnaA-YabA-DnaN PubMed
- part of the replisome: PolC-HolA-HolB-DnaX-DnaN-DnaG-DnaC-DnaI-DnaD-SsbA-DnaE-PriA-DnaB PubMed
- PolY1-DnaN, PolY2-DnaN (required for untargeted mutagenesis) PubMed
- PolY1-PolA-DnaN PubMed
- MutL (C-terminal domain)-DnaN PubMed
- MutS-DnaN PubMed
- DnaE-DnaN PubMed
- DnaN forms dimers PubMed

Localization:
- nucleoid (mid-cell spot) PubMed PubMed
- forms large assemblies on DNA, called "clamp zones" PubMed
- forms foci PubMed

Database entries

Structure:

UniProt: P05649

KEGG entry: [3]

E.C. number: 2.7.7.7

Additional information

Expression and regulation

Operon: dnaA-dnaN PubMed

Expression browser: dnaN PubMed

Sigma factor: SigA PubMed

Regulation: negatively controlled by DnaA PubMed and Spo0A PubMed
- repressed under conditions that trigger sporulation (Spo0A) PubMed

Regulatory mechanism:
- Spo0A: transcription repression PubMed

Additional information:

Biological materials

Mutant:

Expression vector:

lacZ fusion:

GFP fusion: PubMed PubMed

two-hybrid system:

Antibody:

Labs working on this gene/protein

Philippe Noirot, Jouy-en-Josas, France homepage

Your additional remarks

References

Reviews

Justin S Lenhart, Jeremy W Schroeder, Brian W Walsh, Lyle A Simmons
DNA repair and genome maintenance in Bacillus subtilis.
Microbiol Mol Biol Rev: 2012, 76(3);530-64
[PubMed:22933559] [WorldCat.org] [DOI] (I p)

Tsutomu Katayama, Shogo Ozaki, Kenji Keyamura, Kazuyuki Fujimitsu
Regulation of the replication cycle: conserved and diverse regulatory systems for DnaA and oriC.
Nat Rev Microbiol: 2010, 8(3);163-70
[PubMed:20157337] [WorldCat.org] [DOI] (I p)

Original publications

@@ Line 1: / Line 1: @@
-* '''Description:''' AAA+ ATPase, replication initiation protein <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"
 |-
 |style="background:#ABCDEF;" align="center"|'''Gene name'''
-|''dnaA''
+|''dnaN''
 |-
-|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaH, dnaJ, dnaK ''
+|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''' || replication initiation protein
+|style="background:#ABCDEF;" align="center"| '''Product''' || DNA polymerase  III <br/>(beta subunit), beta clamp
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || [[DNA replication]]
+|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=BSU00010 dnaA]
+|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=DnaA DnaA]
+|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''' || 50 kDa, 6.035
+|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 4.718
 |-
-|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1338 bp, 446 aa
+|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1134 bp, 378 aa
 |-
-|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rpmH]]'', ''[[dnaN]]''
+|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dnaA]]'', ''[[yaaA]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00010 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00010 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00010 DNA_with_flanks]
+|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=dnaA_410_1750_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:dnaA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00010]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dnaN_1939_3075_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:DnaN_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00020]]
 |-
 |}
@@ Line 45: / Line 44: @@
 = This gene is a member of the following [[regulons]] =
 {{SubtiWiki regulon|[[Spo0A regulon]]}}
-=The [[DnaA regulon]]=
 =The gene=
 === Basic information ===
-* '''Locus tag:''' BSU00010
+* '''Locus tag:''' BSU00020
 ===Phenotypes of a mutant ===
@@ Line 60: / Line 59: @@
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dnaAN.html]
-* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10065]
+* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10066]
 === Additional information===
 =The protein=
@@ Line 70: / Line 68: @@
 * '''Catalyzed reaction/ biological activity:'''
-** binds multiple regions in the oriC region, required for recruitment of proteins needed to load the replicative helicase [[DnaC]]
+** [[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:''' dnaA family (according to Swiss-Prot)
+* '''Protein family:'''
 * '''Paralogous protein(s):'''
@@ Line 80: / Line 82: @@
 * '''Kinetic information:'''
-* '''Domains:''' AAA+ domain
+* '''Domains:'''
 * '''Modification:'''
@@ Line 87: / Line 89: @@
 * '''Effectors of protein activity:'''
-** [[SirA]] displaces [[DnaA]] from the replication origin {{PubMed|19682252}}
-** [[YabA]] inhibits co-operative binding of DnaA to the ''oriC'' DNA {{PubMed|21895792}}
-** DnaA helix formation (and thus replication initiation) is inhibited by the interaction of either [[Soj]], [[YabA]] or [[DnaN]] with the AAA+ domain of DnaA {{PubMed|23909787,22286949}}
-** interaction with [[DnaD]] inhibits the ability of [[DnaA]] to cooperatively bind to DNA {{PubMed|22821970}}
 * '''[[SubtInteract|Interactions]]:'''
-** [[DnaA]] assembles into a right-handed helical oligomer built upon interactions between neighbouring AAA+ domains {{PubMed|23909787}}
+** [[DnaA]]-[[YabA]]-[[DnaN]] {{PubMed|12060778}}
-** [[Soj]]-[[DnaA]] {{PubMed|22286949}}
+** part of the [[replisome]]: [[PolC]]-[[HolA]]-[[HolB]]-[[DnaX]]-[[DnaN]]-[[DnaG]]-[[DnaC]]-[[DnaI]]-[[DnaD]]-[[SsbA]]-[[DnaE]]-[[PriA]]-[[DnaB]] {{PubMed|20122408}}
-** [[DnaA]]-[[YabA]]  {{PubMed|23909787,12060778}}
+** [[PolY1]]-[[DnaN]], [[PolY2]]-[[DnaN]] (required for untargeted mutagenesis) {{PubMed|15469515}}
-** [[DnaA]]-[[YabA]]-[[DnaN]] {{PubMed|12060778}}
+** [[PolY1]]-[[PolA]]-[[DnaN]] {{PubMed|16045613}}
-** [[DnaA]]-[[DnaD]] {{PubMed|22821970,11222620}}
+** [[MutL]] (C-terminal domain)-[[DnaN]] {{PubMed|21050827}}
-** [[SirA]]-[[DnaA]] {{PubMed|19682252,21239581}}
+** [[MutS]]-[[DnaN]] {{PubMed|20453097}}
-** [[YqaH]]-[[DnaA]] {{PubMed|12060778}}
+** [[DnaE]]-[[DnaN]]  {{PubMed|21958350}}
-** part of the [[primosome]]: [[DnaA]]-[[DnaG]]-[[DnaC]]-[[DnaI]]-[[DnaD]]-[[DnaB]] {{PubMed|22797751}}
+** [[DnaN]] forms dimers {{PubMed|16045613}}
 * '''[[Localization]]:'''
-** throughout the cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/10844689 PubMed]
+** 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 ===
@@ Line 109: / Line 109: @@
 * '''Structure:'''
-* '''UniProt:''' [http://www.uniprot.org/uniprot/P05648 P05648]
+* '''UniProt:''' [http://www.uniprot.org/uniprot/P05649 P05649]
-* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00010]
+* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00020]
-* '''E.C. number:'''
+* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.7.7 2.7.7.7]
 === Additional information===
@@ Line 121: / Line 121: @@
 * '''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=dnaA_410_1750_1 dnaA] {{PubMed|22383849}}
+* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dnaN_1939_3075_1 dnaN] {{PubMed|22383849}}
-* '''[[Sigma factor]]:''' [[SigA]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|2987848}}
-* '''Regulation:'''
+* '''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]
-** 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]
@@ Line 142: / Line 141: @@
 * '''lacZ fusion:'''
-* '''GFP 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:'''
@@ Line 149: / Line 148: @@
 =Labs working on this gene/protein=
-* [[Philippe Noirot]], Jouy-en-Josas, France [http://locus.jouy.inra.fr/cms/index.php?id=18 homepage]
+[[Philippe Noirot]], Jouy-en-Josas, France [http://locus.jouy.inra.fr/cms/index.php?id=18 homepage]
-* [[Peter Graumann]], Freiburg University, Germany [http://www.biologie.uni-freiburg.de/data/bio2/graumann/index.htm homepage]
-* [[Alan Grossman]], MIT, Cambridge, MA, USA
-* [[Heath Murray]], Centre for Bacterial Cell Biology, Newcastle, UK [http://www.ncl.ac.uk/camb/staff/profile/heath.murray homepage]
 =Your additional remarks=
@@ Line 158: / Line 154: @@
 =References=
 ==Reviews==
-<pubmed> 20157337 21035377 21639790 22575476 22797751</pubmed>
+<pubmed> 20157337 22933559 </pubmed>
+== Original publications ==
-==The [[DnaA regulon]]==
+<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> 16120674, </pubmed>
-==Original publications==
-<pubmed>18854156,19011033, 11222620,14651647,17140409 10844689 ,11222620 12060778 16461910 2987848 2168872 11207367, 19737352 19081080 17932079 19968790 19682252 20511500 21097613 21239581 21895792 22286949 22821970 23909787 22396664,21911367</pubmed>
 [[Category:Protein-coding genes]]

Difference between revisions of "Sandbox"

Revision as of 14:26, 11 November 2013

Contents

Categories containing this gene/protein

This gene is a member of the following regulons

The gene

Basic information

Phenotypes of a mutant

Database entries

Additional information

The protein

Basic information/ Evolution

Extended information on the protein

Database entries

Additional information

Expression and regulation

Biological materials

Labs working on this gene/protein

Your additional remarks

References

Reviews

Original publications

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