Difference between revisions of "Sandbox"

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−
* '''Description:''' unknown <br/><br/>
+
* '''Description:''' DNA polymerase X, involved in DNA repair <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'''
−
|''yshB''
+
|''polX''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yshC''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA polymerase X
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || DNA repair
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 19 kDa, 8.531  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 63 kDa, 5.308  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 531 bp, 177 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1710 bp, 570 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[polX]]'', ''[[yshA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mutSB]]'', ''[[yshB]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yshB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yshC_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>
 
|-
 
|-
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yshB.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12326]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12327]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' template-dependent DNA polymerase, fills single nucleotide gaps [http://www.ncbi.nlm.nih.gov/sites/entrez/18938175 PubMed], has intrinsic 3'-5' exonuclease activity for resecting unannealed 3'-termini in gapped DNA substrates [http://www.ncbi.nlm.nih.gov/sites/entrez/18776221 PubMed]
  
−
* '''Protein family:'''
+
* '''Protein family:''' DNA polymerase X family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' monomeric [http://www.ncbi.nlm.nih.gov/sites/entrez/18938175 PubMed]
  
 
* '''Localization:'''
 
* '''Localization:'''
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28600]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28590]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[zapA]]-[[yshB]]''
+
* '''Operon:'''  
  
−
* '''[[[[Sigma factor]]]]:'''  
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
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* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Margarita Salas]], Madrid, Spain [http://www.cbm.uam.es/mkfactory.esdomain/webs/CBMSO/plt_LineasInvestigacion.aspx?IdObjeto=28 link]
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
# Banos et al.  (2008) Characterization of a  Bacillus subtilis 64 kDa DNA polymerase X potentially involved in DNA repair.  ''J. Mol. Biol.'' '''384:''' 1019-1028. [http://www.ncbi.nlm.nih.gov/sites/entrez/18938175 PubMed]
 +
# Banos et al.  (2008) Editing of misaligned 3'-termini by an intrinsic 3'-5' exonuclease activity residing in the PHP domain of a family X DNA polymerase.  ''Nucl. Acids Res.'' '''36:''' 5736-5749. [http://www.ncbi.nlm.nih.gov/sites/entrez/18776221 PubMed]

Revision as of 17:22, 15 April 2009

  • Description: DNA polymerase X, involved in DNA repair

Gene name polX
Synonyms yshC
Essential no
Product DNA polymerase X
Function DNA repair
MW, pI 63 kDa, 5.308
Gene length, protein length 1710 bp, 570 aa
Immediate neighbours mutSB, yshB
Hier soll was neues rein
Genetic context
YshC context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: template-dependent DNA polymerase, fills single nucleotide gaps PubMed, has intrinsic 3'-5' exonuclease activity for resecting unannealed 3'-termini in gapped DNA substrates PubMed
  • Protein family: DNA polymerase X family
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions: monomeric PubMed
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [2]
  • E.C. number:

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

Margarita Salas, Madrid, Spain link

Your additional remarks

References

  1. Banos et al. (2008) Characterization of a Bacillus subtilis 64 kDa DNA polymerase X potentially involved in DNA repair. J. Mol. Biol. 384: 1019-1028. PubMed
  2. Banos et al. (2008) Editing of misaligned 3'-termini by an intrinsic 3'-5' exonuclease activity residing in the PHP domain of a family X DNA polymerase. Nucl. Acids Res. 36: 5736-5749. PubMed
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