Difference between revisions of "Sandbox"

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* '''Description:''' RNase 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'''
−
|''rnc''
+
|''rnpA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''rncS ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || endoribonuclease III
+
|style="background:#ABCDEF;" align="center"| '''Product''' || protein component of RNase P (substrate specificity)
 
|-
 
|-
−
|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''' || cleavage of precursor sequences <br/>from the 5' ends of pre-tRNAs
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 8.076  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 13 kDa, 10.804  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 747 bp, 249 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 348 bp, 116 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[acpA]]'', ''[[smc]]''
+
|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: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:CAB16142&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:rnc_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ThdF_jag_spoIIIJ_rnpA_rpmH_context.png]]
 
  <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/>
  
 
=The gene=
 
=The gene=
Line 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU15930
+
* '''Locus tag:''' BSU41050
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
 
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
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+BG10063]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Endonucleolytic cleavage to 5'-phosphomonoester (according to Swiss-Prot) cleaves both 5'- and 3'-sites of the small cytoplasmic RNA precursor (''[[scr]]'')
+
* '''Catalyzed reaction/ biological activity:''' Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor (according to Swiss-Prot)  
  
−
* '''Protein family:'''
+
* '''Protein family:''' rnpA family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 74: Line 72:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[RnpA]]-[[RpmH]],  RnpA-[[RnpB]]
  
−
* '''Localization:''' cytoplasm (according to Swiss-Prot)
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1A6F 1A6F], [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1A6F 1AF6]  [http://www.ncbi.nlm.nih.gov/sites/entrez/9563955 PubMed]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P51833 P51833]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P25814 P25814]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU15930]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU41050]
  
−
* '''E.C. number:''' 3.1.26.3
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.26.5 3.1.26.5]
  
 
=== Additional information===
 
=== Additional information===
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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]
+
[[Roland Hartmann]], Marburg University, Germany [http://www.pharmazie.uni-marburg.de/pharmchem/akhartmann/ag_hartmann.htm homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>9393702 11123676 7527387 9677377 17576666, </pubmed>
+
<pubmed>11454206 9563955, </pubmed>
−
# 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]
+
# 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]
−
# 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]
+
# 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]
−
# 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 14:33, 8 June 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

  • Locus tag: BSU41050

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: Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor (according to Swiss-Prot)
  • Protein family: rnpA family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • 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

A Hansen, T Pfeiffer, T Zuleeg, S Limmer, J Ciesiolka, R Feltens, R K Hartmann
Exploring the minimal substrate requirements for trans-cleavage by RNase P holoenzymes from Escherichia coli and Bacillus subtilis.
Mol Microbiol: 2001, 41(1);131-43
[PubMed:11454206] [WorldCat.org] [DOI] (P p)

T Stams, S Niranjanakumari, C A Fierke, D W Christianson
Ribonuclease P protein structure: evolutionary origins in the translational apparatus.
Science: 1998, 280(5364);752-5
[PubMed:9563955] [WorldCat.org] [DOI] (P p)

  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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