Difference between revisions of "PolY2"

From SubtiWiki
Jump to: navigation, search
 
(38 intermediate revisions by 7 users not shown)
Line 13: Line 13:
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || UV-targeted mutagenesis
 
|style="background:#ABCDEF;" align="center"|'''Function''' || UV-targeted mutagenesis
 +
|-
 +
|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=BSU23710 polY2]
 +
|-
 +
|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=PolY2 PolY2]
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 9.532   
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 9.532   
Line 20: Line 24:
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqjX]]'', ''[[yqzH]]''
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqjX]]'', ''[[yqzH]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yqjW_nucleotide.txt    Gene sequence     (+200bp)  ]'''
+
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU23710 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU23710 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU23710 DNA_with_flanks]
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yqjW_protein.txt Protein sequence]'''
 
 
|-
 
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:yqjW_context.gif]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:yqjW_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=polYB_2464562_2465800_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:polY2_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU23710]]
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/>
  
−
<br/><br/>
+
= [[Categories]] containing this gene/protein =
 +
{{SubtiWiki category|[[DNA repair/ recombination]]}}
 +
 
 +
= This gene is a member of the following [[regulons]] =
 +
{{SubtiWiki regulon|[[LexA regulon]]}}
  
 
=The gene=
 
=The gene=
Line 35: Line 49:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Locus tag:''' BSU23710
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU23710&redirect=T BSU23710]
  
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqjWX.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqjWX.html]
Line 46: Line 61:
  
 
=== Additional information===
 
=== Additional information===
 +
 +
  
  
Line 52: Line 69:
 
=== 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)
  
−
* '''Protein family:'''
+
* '''Protein family:''' DNA polymerase type-Y family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[PolY1]], [[UvrX]], [[YozK]]-[[YobH]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 70: Line 87:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''[[SubtInteract|Interactions]]:'''
 +
** [[PolY2]]-[[DnaN]] (required for untargeted mutagenesis) {{PubMed|15469515}}
 +
** [[PolA]]-[[PolY2]] {{PubMed|16045613}}
  
−
* '''Localization:'''
+
* '''[[Localization]]:'''
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU23710&redirect=T BSU23710]
  
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:'''
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/P54560 P54560]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23710]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23710]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 88: Line 108:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[polY2]]-[[yqjX]]'' (according to [http://dbtbs.hgc.jp/COG/prom/yqjWX.html DBTBS])
 +
 
 +
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=polYB_2464562_2465800_-1 polY2] {{PubMed|22383849}}
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
 +
** induced upon DNA damage ([[LexA]]) {{PubMed|15469515,16267290}}
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
 +
** [[LexA]]: transcription repression {{PubMed|15469515,16267290}}
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' GP1505 (''polY2''::''kan''), available in [[Stülke]] lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 117: Line 141:
  
 
=References=
 
=References=
 +
==Reviews==
 +
<pubmed> 22933559 </pubmed>
 +
== Original publications ==
 +
<pubmed>16267290,  12644484 15469515 16045613 19924481 23686288 </pubmed>
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
[[Category:Protein-coding genes]]

Latest revision as of 14:08, 2 April 2014

  • Description: translesion synthesis (TLS-) DNA polymerase Y2

Gene name polY2
Synonyms yqjW
Essential no
Product translesion synthesis (TLS-) DNA polymerase Y2
Function UV-targeted mutagenesis
Gene expression levels in SubtiExpress: polY2
Interactions involving this protein in SubtInteract: PolY2
MW, pI 45 kDa, 9.532
Gene length, protein length 1236 bp, 412 aa
Immediate neighbours yqjX, yqzH
Sequences Protein DNA DNA_with_flanks
Genetic context
YqjW context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
PolY2 expression.png















Categories containing this gene/protein

DNA repair/ recombination

This gene is a member of the following regulons

LexA regulon

The gene

Basic information

  • Locus tag: BSU23710

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1) (according to Swiss-Prot)
  • Protein family: DNA polymerase type-Y family (according to Swiss-Prot)

Extended information on the protein

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

Database entries

  • Structure:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant: GP1505 (polY2::kan), available in Stülke lab
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

Reviews

Original publications

Richard T Pomerantz, Isabel Kurth, Myron F Goodman, Mike E O'Donnell
Preferential D-loop extension by a translesion DNA polymerase underlies error-prone recombination.
Nat Struct Mol Biol: 2013, 20(6);748-55
[PubMed:23686288] [WorldCat.org] [DOI] (I p)

Andrea M Rivas-Castillo, Ronald E Yasbin, E Robleto, Wayne L Nicholson, Mario Pedraza-Reyes
Role of the Y-family DNA polymerases YqjH and YqjW in protecting sporulating Bacillus subtilis cells from DNA damage.
Curr Microbiol: 2010, 60(4);263-7
[PubMed:19924481] [WorldCat.org] [DOI] (I p)

Nora Au, Elke Kuester-Schoeck, Veena Mandava, Laura E Bothwell, Susan P Canny, Karen Chachu, Sierra A Colavito, Shakierah N Fuller, Eli S Groban, Laura A Hensley, Theresa C O'Brien, Amish Shah, Jessica T Tierney, Louise L Tomm, Thomas M O'Gara, Alexi I Goranov, Alan D Grossman, Charles M Lovett
Genetic composition of the Bacillus subtilis SOS system.
J Bacteriol: 2005, 187(22);7655-66
[PubMed:16267290] [WorldCat.org] [DOI] (P p)

Stéphane Duigou, S Dusko Ehrlich, Philippe Noirot, Marie-Françoise Noirot-Gros
DNA polymerase I acts in translesion synthesis mediated by the Y-polymerases in Bacillus subtilis.
Mol Microbiol: 2005, 57(3);678-90
[PubMed:16045613] [WorldCat.org] [DOI] (P p)

Stéphane Duigou, S Dusko Ehrlich, Philippe Noirot, Marie-Françoise Noirot-Gros
Distinctive genetic features exhibited by the Y-family DNA polymerases in Bacillus subtilis.
Mol Microbiol: 2004, 54(2);439-51
[PubMed:15469515] [WorldCat.org] [DOI] (P p)

Huang-Mo Sung, Gabriel Yeamans, Christian A Ross, Ronald E Yasbin
Roles of YqjH and YqjW, homologs of the Escherichia coli UmuC/DinB or Y superfamily of DNA polymerases, in stationary-phase mutagenesis and UV-induced mutagenesis of Bacillus subtilis.
J Bacteriol: 2003, 185(7);2153-60
[PubMed:12644484] [WorldCat.org] [DOI] (P p)

Retrieved from "https://subtiwiki.uni-goettingen.de/wiki//index.php?title=PolY2&oldid=200756"