Difference between revisions of "Sandbox"

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* '''Description:''' RNase J2<br/><br/>
+
* '''Description:''' signal peptide peptidase required for efficient processing of pre-proteins <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'''
−
|''rnjB ''
+
|''tepA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ymfA''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ymfB, ylxI ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || RNase J2
+
|style="background:#ABCDEF;" align="center"| '''Product''' || signal peptide peptidase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA processing and degradation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || protein secretion
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 9.18  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 24 kDa, 5.575  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1545 bp, 515 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 669 bp, 223 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dapA]]'', ''[[tepA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rnjB]]'', ''[[spoIIIE]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13551&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13552&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:tepA_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ymfA_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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__TOC__
 
__TOC__
  
−
<br/><br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
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* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13422]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11055]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' endoribonuclease, involved in processing of ''[[thrS]]'' mRNA
+
* '''Catalyzed reaction/ biological activity:'''  
  
 
* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[RnjA]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[RnjA]]-[[RnjB]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
+
* '''Interactions:'''
  
 
* '''Localization:''' Cytoplasm
 
* '''Localization:''' Cytoplasm
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=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do;jsessionid=8B071C0C81B11ADEBA3DDC3FF3395811?structureId=3BK1 3BK1] (RNase J from ''Thermus thermophilus'') [http://www.pdb.org/pdb/explore/explore.do?structureId=3BK2 3BK2] (RNase J from ''Thermus thermophilus'', complex with UMP)
+
* '''Structure:'''
 +
 
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16780]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16790]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
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=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP45, GP1113 (spc), available in [[Stülke]] lab
+
* '''Mutant:''' GP1120 (spc), available in the [[Stülke]] lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 109: Line 108:
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+
* '''two-hybrid system:'''  
  
 
* '''Antibody:'''
 
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Harald Putzer]], IBPC Paris, France [http://www.ibpc.fr/UPR9073/putzer/recherches_harald.htm Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
# Even, S., Pellegrini, O., Zig, L., Labas, V., Vinh, J., Brechemmier-Baey, D., and Putzer, H. (2005) Ribonucleases J1 and J2: Two novel endoribonucleases in B. subtilis with functional  homology to E. coli RNase E. Nucl Acids Res 33, 2141-2152. [http://www.ncbi.nlm.nih.gov/sites/entrez/15831787 PubMed]
 
−
# de la Sierra-Gallay IL, Zig L, Jamalli A, Putzer H. (2008 Structural insights into the dual activity of RNase J. Nat. Struct. Mol. Biol. 15:206-212. [http://www.ncbi.nlm.nih.gov/sites/entrez/18204464 PubMed]
 
−
# Mäder, U., Zig, L., Kretschmer, J., Homuth, G., and Putzer, H. (2008) mRNA processing by RNases J1 and J2 affects Bacillus subtilis gene expression on a global scale. Mol Microbiol 70, 183-196. [http://www.ncbi.nlm.nih.gov/sites/entrez/18713320 PubMed]
 
−
# Commichau, F. M., Rothe, F. M., Herzberg, C., Wagner, E., Hellwig, D., Lehnik-Habrink, M., Hammer, E., Völker, U. & Stülke, J. (2009) Novel activities of glycolytic enzymes in Bacillus subtilis: Interactions with essential proteins involved in mRNA processing. Mol. Cell. Proteomics in press [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
 
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 02:21, 30 April 2009

  • Description: signal peptide peptidase required for efficient processing of pre-proteins

Gene name tepA
Synonyms ymfB, ylxI
Essential no
Product signal peptide peptidase
Function protein secretion
MW, pI 24 kDa, 5.575
Gene length, protein length 669 bp, 223 aa
Immediate neighbours rnjB, spoIIIE
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
TepA 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:
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

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

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: GP1120 (spc), available in the Stülke lab
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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