Difference between revisions of "Sandbox"

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* '''Description:''' RNase III<br/><br/>
+
* '''Description:''' 16S rRNA processing protein, RNase <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'''
−
|''rnc''
+
|''rimM''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''rncS ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ylqE ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || endoribonuclease III
+
|style="background:#ABCDEF;" align="center"| '''Product''' || 16S rRNA processing protein, RNase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || cleaves both 5'- and 3'-sites of the small cytoplasmic RNA precursor (''[[scr]]'')
+
|style="background:#ABCDEF;" align="center"|'''Function''' || maturation of 16S rRNA
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 8.076  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 20 kDa, 5.222  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 747 bp, 249 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 522 bp, 174 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[acpA]]'', ''[[smc]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ylqD]]'', ''[[trmD]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13466&#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:CAB13475&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:rnc_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:rimM_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>
 
|-
 
|-
Line 38: Line 38:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
−
 
−
''rnc'' is essential [http://www.ncbi.nlm.nih.gov/sites/entrez/11123676 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rnc-smc-ftsY.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11537]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13404]
  
 
=== Additional information===
 
=== Additional information===
Line 56: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' cleaves both 5'- and 3'-sites of the small cytoplasmic RNA precursor (''[[scr]]'')
+
* '''Catalyzed reaction/ biological activity:'''  
  
 
* '''Protein family:'''
 
* '''Protein family:'''
Line 84: Line 80:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU15930]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16020]
  
−
* '''E.C. number:''' 3.1.26.3
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
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* '''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=
−
[[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]
 
−
 
−
[[Ciaran Condon]], IBPC, Paris, France [http://www.ibpc.fr/UPR9073/condon/index_en.html Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 125: Line 118:
 
=References=
 
=References=
  
−
# Wang, W. & Bechhofer, D. H. (1997). ''Bacillus subtilis'' RNase III gene: cloning, function of the gene in ''Escherichia coli'', and construction of ''Bacillus subtilis'' strains with altered ''rnc'' loci. J Bacteriol 179, 7379-7385. [http://www.ncbi.nlm.nih.gov/sites/entrez/9393702 PubMed]
 
−
# Herskovitz, M. A. & Bechhofer, D. H. (2000). Endoribonuclease RNase III is essential in ''Bacillus subtilis''. Mol Microbiol 38:1027-1033. [http://www.ncbi.nlm.nih.gov/sites/entrez/11123676 PubMed]
 
−
# Mitra, S. & Bechhofer, D. H. (1994). Substrate specificity of an RNase III-like activity from ''Bacillus subtilis''. J Biol Chem 269:31450-31456. [http://www.ncbi.nlm.nih.gov/sites/entrez/7527387 PubMed]
 
−
# Oguro, A., Kakeshita, H., Nakamura, K., Yamane, K., Wang, W. & Bechhofer, D. H. (1998). ''Bacillus subtilis'' RNase III cleaves both 5'- and 3'-sites of the small cytoplasmic RNA precursor. J Biol Chem 273:19542-19547. [http://www.ncbi.nlm.nih.gov/sites/entrez/9677377 PubMed]
 
−
# Yao, S., Blaustein, J. B. & Bechhofer, D. H. (2007). Processing of ''Bacillus subtilis'' small cytoplasmic RNA: evidence for an additional endonuclease cleavage site. Nucleic Acids Res. 35:4464-4473. [http://www.ncbi.nlm.nih.gov/sites/entrez/17576666 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 02:16, 30 April 2009

  • Description: 16S rRNA processing protein, RNase

Gene name rimM
Synonyms ylqE
Essential no
Product 16S rRNA processing protein, RNase
Function maturation of 16S rRNA
MW, pI 20 kDa, 5.222
Gene length, protein length 522 bp, 174 aa
Immediate neighbours ylqD, trmD
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
RimM 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:
  • 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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