Difference between revisions of "Sandbox"

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* '''Description:''' 4.5 S RNA<br/><br/>
+
* '''Description:''' DNA polymerase  III (gamma and tau subunits) part of the clamp-loader complex and the [[replisome]] <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''scr''
+
|''dnaX''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaH, dna-8132 ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || small cytoplasmic RNA (scRNA, 4.5S RNA),
+
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA polymerase  III (gamma and tau subunits)
−
 
+
|-
−
[[signal recognition particle]]-like ([[SRP]]) component
+
|style="background:#ABCDEF;" align="center"|'''Function''' || [[DNA replication]]
 +
|-
 +
|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=BSU00190 dnaX]
 +
|-
 +
|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=DnaX DnaX]
 +
|-
 +
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62 kDa, 5.488 
 +
|-
 +
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1689 bp, 563 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || presecretory protein translocation
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[scr]]'', ''[[yaaK]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this RNA in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=Scr Scr]
+
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00190 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00190 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00190 DNA_with_flanks]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaJ]]'', ''[[dnaX]]''
 
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/scr_nucleotide.txt    Gene sequence      (+200bp)  ]'''
 
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/scr_protein.txt Protein sequence]'''
 
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:scr_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:dnaX_context.gif]]
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <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=dnaX_26814_28505_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:dnaX_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00190]]
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
−
 
+
<br/><br/><br/><br/>
−
<br/><br/><br/><br/><br/><br/>
+
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/>
  
 
= [[Categories]] containing this gene/protein =
 
= [[Categories]] containing this gene/protein =
−
{{SubtiWiki category|[[protein secretion]]}},
+
{{SubtiWiki category|[[DNA replication]]}},
−
{{SubtiWiki category|[[essential genes]]}},
+
{{SubtiWiki category|[[essential genes]]}}
−
{{SubtiWiki category|[[ncRNA]]}}
 
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
Line 44: Line 52:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:'''
+
* '''Locus tag:''' BSU00190
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
* the gene is essential {{PubMed|7506707}}
+
 
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 +
 
 
=== Database entries ===
 
=== Database entries ===
  
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG00095]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10083]
 +
 
 +
=== Additional information===
  
−
* '''Structure:'''
 
  
−
=== Additional information===
 
  
  
−
=The RNA=
+
=The protein=
  
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
 +
** Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1) (according to Swiss-Prot)
 +
** required for bacteriophage SPP1 replication {{PubMed|23268446}}
 +
 +
* '''Protein family:'''
 +
 +
* '''Paralogous protein(s):'''
 +
 +
=== Extended information on the protein ===
 +
 +
* '''Kinetic information:'''
  
−
=== Extended information on the RNA===
+
* '''Domains:'''
  
−
* '''Kinetic information'''
+
* '''Modification:'''
  
−
* '''[[SubtInteract|Interactions]]:'''  
+
* '''Cofactor(s):'''
−
** [[Scr]]-[[Ffh]] in the [[signal recognition particle]]
 
  
−
* '''[[Localization]]'''
+
* '''Effectors of protein activity:'''
 +
 
 +
* '''[[SubtInteract|Interactions]]:'''
 +
** [[DnaX]]-[[DnaB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/14757052 PubMed]
 +
** [[DnaX]]-[[DnaC]] {{PubMed|23525462}}
 +
** [[DnaX]](3)-[[HolA]]-[[HolB]], the clamp-loader complex {{PubMed|23525462}}
 +
** part of the [[replisome]]: [[PolC]]-[[HolA]]-[[HolB]]-[[DnaX]]-[[DnaN]]-[[DnaG]]-[[DnaC]]-[[DnaI]]-[[DnaD]]-[[SsbA]]-[[DnaE]]-[[PriA]]-[[DnaB]] {{PubMed|20122408}}
 +
 
 +
* '''[[Localization]]:'''
 +
** forms foci {{PubMed|21958350}}
 +
** Nucleoid (Mid-cell) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure''':  
+
* '''Structure:'''
 +
 
 +
* '''UniProt:''' [http://www.uniprot.org/uniprot/P09122 P09122]
 +
 
 +
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00190]
 +
 
 +
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.7.7 2.7.7.7]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[yaaJ]]-[[scr]],  [[scr]]''
+
* '''Operon:'''
 +
 
 +
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dnaX_26814_28505_1 dnaX] {{PubMed|22383849}}
  
−
* '''Sigma factor:''' [[SigA]] (both promoters)
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 90: Line 127:
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:''' transcribed as 354 nt precursor, cleaved at the 5' end by [[rnc| RNase III]] and at the 3' site by [[rnjA| RNase J1]] to yield a 275 nt molecule, final trimming to 271 nt sc RNA by [[rph| RNase PH]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17576666 PubMed]
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 99: Line 136:
 
          
 
          
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
 +
 +
* '''GFP fusion:'''
 +
 +
* '''two-hybrid system:'''
 +
 +
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
  
 
=References=
 
=References=
 +
<pubmed> 16479537, 19415803, 14757052, 12974630 1703271, 12466528 20122408 23525462 23268446,21958350</pubmed>
  
−
<pubmed>9346318,2468993,17576666, 1372600,7506707 1383945 7538759 10224127 9677377 8662730 10222262</pubmed>
+
[[Category:Protein-coding genes]]
−
 
 
−
[[Category:small RNA]]
 

Revision as of 14:54, 11 November 2013

  • Description: DNA polymerase III (gamma and tau subunits) part of the clamp-loader complex and the replisome

Gene name dnaX
Synonyms dnaH, dna-8132
Essential yes PubMed
Product DNA polymerase III (gamma and tau subunits)
Function DNA replication
Gene expression levels in SubtiExpress: dnaX
Interactions involving this protein in SubtInteract: DnaX
MW, pI 62 kDa, 5.488
Gene length, protein length 1689 bp, 563 aa
Immediate neighbours scr, yaaK
Sequences Protein DNA DNA_with_flanks
Genetic context
DnaX context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
DnaX expression.png















Categories containing this gene/protein

DNA replication, essential genes

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag: BSU00190

Phenotypes of a mutant

essential PubMed

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
    • Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1) (according to Swiss-Prot)
    • required for bacteriophage SPP1 replication PubMed
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:

Database entries

  • Structure:
  • KEGG entry: [2]

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

José P Afonso, Kiran Chintakayala, Chatrudee Suwannachart, Svetlana Sedelnikova, Kevin Giles, John B Hoyes, Panos Soultanas, John B Rafferty, Neil J Oldham
Insights into the structure and assembly of the Bacillus subtilis clamp-loader complex and its interaction with the replicative helicase.
Nucleic Acids Res: 2013, 41(9);5115-26
[PubMed:23525462] [WorldCat.org] [DOI] (I p)

Elena M Seco, John C Zinder, Carol M Manhart, Ambra Lo Piano, Charles S McHenry, Silvia Ayora
Bacteriophage SPP1 DNA replication strategies promote viral and disable host replication in vitro.
Nucleic Acids Res: 2013, 41(3);1711-21
[PubMed:23268446] [WorldCat.org] [DOI] (I p)

Andrew D Klocko, Jeremy W Schroeder, Brian W Walsh, Justin S Lenhart, Margery L Evans, Lyle A Simmons
Mismatch repair causes the dynamic release of an essential DNA polymerase from the replication fork.
Mol Microbiol: 2011, 82(3);648-63
[PubMed:21958350] [WorldCat.org] [DOI] (I p)

Glenn M Sanders, H Garry Dallmann, Charles S McHenry
Reconstitution of the B. subtilis replisome with 13 proteins including two distinct replicases.
Mol Cell: 2010, 37(2);273-81
[PubMed:20122408] [WorldCat.org] [DOI] (I p)

Kiran Chintakayala, Cristina Machón, Anna Haroniti, Marilyn A Larson, Steven H Hinrichs, Mark A Griep, Panos Soultanas
Allosteric regulation of the primase (DnaG) activity by the clamp-loader (tau) in vitro.
Mol Microbiol: 2009, 72(2);537-49
[PubMed:19415803] [WorldCat.org] [DOI] (I p)

Jean-Christophe Meile, Ling Juan Wu, S Dusko Ehrlich, Jeff Errington, Philippe Noirot
Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory.
Proteomics: 2006, 6(7);2135-46
[PubMed:16479537] [WorldCat.org] [DOI] (P p)

Anna Haroniti, Christopher Anderson, Zara Doddridge, Laurence Gardiner, Clive J Roberts, Stephanie Allen, Panos Soultanas
The clamp-loader-helicase interaction in Bacillus. Atomic force microscopy reveals the structural organisation of the DnaB-tau complex in Bacillus.
J Mol Biol: 2004, 336(2);381-93
[PubMed:14757052] [WorldCat.org] [DOI] (P p)

A Haroniti, R Till, M C M Smith, P Soultanas
Clamp-loader-helicase interaction in Bacillus. Leucine 381 is critical for pentamerization and helicase binding of the Bacillus tau protein.
Biochemistry: 2003, 42(37);10955-64
[PubMed:12974630] [WorldCat.org] [DOI] (P p)

María I Martínez-Jiménez, Pablo Mesa, Juan C Alonso
Bacillus subtilis tau subunit of DNA polymerase III interacts with bacteriophage SPP1 replicative DNA helicase G40P.
Nucleic Acids Res: 2002, 30(23);5056-64
[PubMed:12466528] [WorldCat.org] [DOI] (I p)

J C Struck, J C Alonso, H Y Toschka, V A Erdmann
The Bacillus subtilis small cytoplasmic RNA gene and 'dnaX' map near the chromosomal replication origin.
Mol Gen Genet: 1990, 222(2-3);470-2
[PubMed:1703271] [WorldCat.org] [DOI] (P p)

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