Difference between revisions of "Sandbox"

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* '''Description:''' membrane protein translocase, essential for sigma-G activity at stage III <br/><br/>
+
* '''Description:''' protein component of ribonuclease P  <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'''
−
|''spoIIIJ''
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|''rnpA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spo0J87 ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || membrane protein translocase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || protein component of RNase P (substrate specificity)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || control of SigG activity
+
|style="background:#ABCDEF;" align="center"|'''Function''' || cleavage of precursor sequences <br/>from the 5' ends of pre-tRNAs
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 9.992  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 13 kDa, 10.804  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 783 bp, 261 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 348 bp, 116 aa  
−
|-
 
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[jag]]'', ''[[rnpA]]''
 
−
|-
 
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16141&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
 
|-
 
|-
 +
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spoIIIJ]]'', ''[[rpmH]]''
 
|-
 
|-
 +
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16142&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ThdF_jag_spoIIIJ_rnpA_rpmH_context.png]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ThdF_jag_spoIIIJ_rnpA_rpmH_context.png]]
Line 31: Line 29:
 
__TOC__
 
__TOC__
  
−
<br/><br/><br/><br/>
+
<br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 40: Line 38:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/spoIIIJ-jag.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10062]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10063]
  
 
=== Additional information===
 
=== Additional information===
Line 58: Line 58:
 
* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[YqjG]], one of the two proteins has to be present for viability [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 PubMed]
+
* '''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:''' [[SpoIIIAE]]-[[SpoIIIJ]],  
+
* '''Interactions:''' [[RnpA]]-[[RpmH]], RnpA-[[RnpB]]
  
−
* '''Localization:''' membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1A6F 1AF6]  [http://www.ncbi.nlm.nih.gov/sites/entrez/9563955 PubMed]
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU41040]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU41050]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.26.5 3.1.26.5]
  
 
=== Additional information===
 
=== Additional information===
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* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 116: Line 115:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Roland Hartmann]], Marburg University, Germany [http://www.pharmazie.uni-marburg.de/pharmchem/akhartmann/ag_hartmann.htm homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 121: Line 122:
 
=References=
 
=References=
  
−
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
# Hansen, A., Pfeiffer, T., Zuleeg, T., Limmer, S., Ciesiolka, J., Feltens, R. & Hartmann, R. K. (2001). Exploring the minimal substrate requirements for trans-cleavage by RNase P holoenzyme from ''Escherichia coli'' and ''Bacillus subtilis''. Mol Microbiol 41, 131-143. [http://www.ncbi.nlm.nih.gov/sites/entrez/11454206 PubMed]
−
# Thomaides, H. B., Davison, E. J., Burston, L., Johnson, H., Brown, D. R., Hunt, A. C., Errington, J., and Czaplewski, L. (2007) Essential bacterial functions encoded by gene pairs. J Bacteriol 189, 591-602. [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 PubMed]
+
# Stams T, Niranjanakumari S, Fierke CA, Christianson DW (1998) Ribonuclease P protein structure: evolutionary origins in the translational apparatus.''Science'' '''280:''' 752-755. [http://www.ncbi.nlm.nih.gov/sites/entrez/9563955 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 00:26, 28 April 2009

  • Description: protein component of ribonuclease P

Gene name rnpA
Synonyms
Essential yes PubMed
Product protein component of RNase P (substrate specificity)
Function cleavage of precursor sequences
from the 5' ends of pre-tRNAs
MW, pI 13 kDa, 10.804
Gene length, protein length 348 bp, 116 aa
Immediate neighbours spoIIIJ, rpmH
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
ThdF jag spoIIIJ rnpA rpmH context.png
This image was kindly provided by SubtiList




The gene

Basic information

  • Coordinates:

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:
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Swiss prot entry:
  • KEGG entry: [2]

Additional information

Expression and regulation

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

Biological materials

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

Labs working on this gene/protein

Roland Hartmann, Marburg University, Germany homepage

Your additional remarks

References

  1. Hansen, A., Pfeiffer, T., Zuleeg, T., Limmer, S., Ciesiolka, J., Feltens, R. & Hartmann, R. K. (2001). Exploring the minimal substrate requirements for trans-cleavage by RNase P holoenzyme from Escherichia coli and Bacillus subtilis. Mol Microbiol 41, 131-143. PubMed
  2. Stams T, Niranjanakumari S, Fierke CA, Christianson DW (1998) Ribonuclease P protein structure: evolutionary origins in the translational apparatus.Science 280: 752-755. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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