Difference between revisions of "Sandbox"

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* '''Description:''' required for cell shape determination <br/><br/>
+
* '''Description:''' RNase PH<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'''
−
|''rodZ''
+
|''rph''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ymfM ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || morphogenic protein
+
|style="background:#ABCDEF;" align="center"| '''Product''' || exoribonuclease PH (EC 2.7.7.56)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || required for cell shape determination
+
|style="background:#ABCDEF;" align="center"|'''Function''' || 3'-5' exoribonuclease
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 4.679  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 4.888  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 639 bp, 213 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 735 bp, 245 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ymfL]]'', ''[[pgsA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ysnA]]'', ''[[gerM]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13564&#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:CAB14797&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:rph_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ymfM_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=
Line 37: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU16910
+
* '''Locus tag:''' BSU28370
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 45: Line 43:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13433]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10357]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' tRNA(n+1) + phosphate = tRNA(n) + a nucleoside diphosphate (according to Swiss-Prot) 3'-5' exoribonuclease
  
−
* '''Protein family:'''
+
* '''Protein family:''' RNase PH family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1OYS 1OYS]
  
−
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P28619 P28619]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16910]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28370]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.7.56 2.7.7.56]
  
 
=== Additional information===
 
=== Additional information===
−
overexpression results in growth inhibition in minimal medium (in the absence of Mg2+ )
 
  
 
=Expression and regulation=
 
=Expression and regulation=
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* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 117: Line 114:
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
  
−
[[Adriano Henriques]], Lisbon, Portugal  [http://www.itqb.unl.pt/research/biology/microbial-development homepage]
+
[[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=
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=References=
 
=References=
  
−
<pubmed>19164570, </pubmed>
+
<pubmed>17576666 15805522, </pubmed>
−
# Alyahya et al. (2009) RodZ, a component of the bacterial core morphogenic apparatus. Proc. Natl. Acad. Sci. USA 106: 1239-1244. [http://www.ncbi.nlm.nih.gov/sites/entrez/19164570 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]
 +
# Oussenko, I. A., Abe, T., Ujiie, H., Muto, A. & Bechhofer, D. H. (2005). Participation of 3'-to-5' exoribonucleases in the turnover of ''Bacillus subtilis'' mRNA. J Bacteriol 187:2758-2767. [http://www.ncbi.nlm.nih.gov/sites/entrez/15805522 PubMed]
 +
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 13:34, 8 June 2009

  • Description: RNase PH

Gene name rph
Synonyms
Essential no
Product exoribonuclease PH (EC 2.7.7.56)
Function 3'-5' exoribonuclease
MW, pI 26 kDa, 4.888
Gene length, protein length 735 bp, 245 aa
Immediate neighbours ysnA, gerM
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
Rph context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU28370

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: tRNA(n+1) + phosphate = tRNA(n) + a nucleoside diphosphate (according to Swiss-Prot) 3'-5' exoribonuclease
  • Protein family: RNase PH family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

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

David Bechhofer, Mount Sinai School, New York, USA Homepage

Ciaran Condon, IBPC, Paris, France Homepage

Your additional remarks

References

Shiyi Yao, Joshua B Blaustein, David H Bechhofer
Processing of Bacillus subtilis small cytoplasmic RNA: evidence for an additional endonuclease cleavage site.
Nucleic Acids Res: 2007, 35(13);4464-73
[PubMed:17576666] [WorldCat.org] [DOI] (I p)

Irina A Oussenko, Teppei Abe, Hiromi Ujiie, Akira Muto, David H Bechhofer
Participation of 3'-to-5' exoribonucleases in the turnover of Bacillus subtilis mRNA.
J Bacteriol: 2005, 187(8);2758-67
[PubMed:15805522] [WorldCat.org] [DOI] (P p)

  1. 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. PubMed
  2. Oussenko, I. A., Abe, T., Ujiie, H., Muto, A. & Bechhofer, D. H. (2005). Participation of 3'-to-5' exoribonucleases in the turnover of Bacillus subtilis mRNA. J Bacteriol 187:2758-2767. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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