Difference between revisions of "Sandbox"

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−
* '''Description:''' transcriptional activator of arginine utilization operons <br/><br/>
+
* '''Description:''' ornithine transaminase <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'''
−
|''rocR''
+
|''rocD''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|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''' || transcriptional regulator
+
|style="background:#ABCDEF;" align="center"| '''Product''' || ornithine transaminase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || transcriptional activator of arginine utilization operons
+
|style="background:#ABCDEF;" align="center"|'''Function''' || arginine, ornithine and citrulline utilization
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52.6 kDa, 6.08
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 4.894 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1383 bp, 461 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1203 bp, 401 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rocD]]'', ''[[yyxA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rocE]]'', ''[[rocR]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:rocR_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:rocD_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 30: Line 30:
  
 
<br/><br/>
 
<br/><br/>
−
 
  
 
=The gene=
 
=The gene=
Line 36: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 4144771 - 4146153
+
* '''Coordinates:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 42: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rocR.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rocDEF.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10723]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10722]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' transcription activation at [[SigL]]-dependent promoters of ''[[rocA|rocABC]]'', ''[[rocD|rocDEF]]'', and ''[[rocG]]''
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' [[SigL | Sigma-54]] interacting transcription activator
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
−
**[[SigL | Sigma-54]] factor interaction domain (143–372)
 
−
**2x nucleotid-binding domain (171–178),(233–242)
 
−
**HTH motif (434–453)
 
  
 
* '''Modification:'''
 
* '''Modification:'''
  
−
* '''Cofactor(s):''' ornithine or citrulline are required for RocR-dependent transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/9194709  PubMed]
+
* '''Cofactor(s):'''
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' RocR-[[SigL]]
+
* '''Interactions:'''
  
 
* '''Localization:'''
 
* '''Localization:'''
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P38022]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40350]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40340]
 +
 
 +
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''rocR''
+
* '''Operon:''' ''[[rocD]]-[[rocE]]-[[rocF]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/7540694 PubMed]
  
−
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+7540694 PubMed]
+
* '''[[Sigma factor]]:''' [[SigL]] [http://www.ncbi.nlm.nih.gov/sites/entrez/7540694 PubMed]  
  
−
* '''Regulation:''' autoregulation by [[RocR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+7540694 PubMed]
+
* '''Regulation:''' induced by arginine ([[RocR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/7540694 PubMed]  
  
−
* '''Regulatory mechanism:''' autorepression
+
* '''Regulatory mechanism:''' [[RocR]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/7540694 PubMed]
  
 
* '''Additional information:'''
 
* '''Additional information:'''
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=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' QB5533 (aphA3), from [[Michel Debarbouille]], available in [[Stülke]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
−
+
       
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
 +
 +
* '''two-hybrid system:'''
  
 
* '''Antibody:'''
 
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Michel Debarbouille]], Pasteur Institute, Paris, France [http://www.pasteur.fr/ip/easysite/go/03b-00000m-0ob/recherche/departements-scientifiques/microbiologie/unites-et-groupes/unite-de-biologie-des-bacteries-pathogenes-a-gram-positif/les-membres-de-l-equipe Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
# Belitsky BR, Sonenshein AL (1998) Role and regulation of Bacillus subtilis glutamate dehydrogenase genes. J Bacteriol 180:6298-6305. [http://www.ncbi.nlm.nih.gov/sites/entrez/9829940  PubMed]
+
# Gardan R, Rapoport G, Débarbouillé M. (1995) Expression of the rocDEF operon involved in arginine catabolism in Bacillus subtilis. ''J Mol Biol. '' '''Jun 23;249(5):''' 843-56. [http://www.ncbi.nlm.nih.gov/sites/entrez/7540694 PubMed]  
−
# Belitsky BR, Sonenshein, AL: (1999) An enhancer element located downstream of the major glutamate dehydrogenase gene of Bacillus subtilis. Proc Natl Acad Sci USA , 96:10290-10295. [http://www.ncbi.nlm.nih.gov/sites/entrez/10468601  PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Gardan R, Rapoport G, Débarbouillé M:(1997) Role of the transcriptional activator RocR in the arginine-degradation pathway of Bacillus subtilis. Mol Microbiol , 24:825-837. [http://www.ncbi.nlm.nih.gov/sites/entrez/9194709  PubMed]
 
−
# Gardan R, Rapoport G, Débarbouillé M: (1995) Expression of the rocDEF operon involved in arginine catabolism in Bacillus subtilis. J Mol Biol , 249:843-856. [http://www.ncbi.nlm.nih.gov/sites/entrez/7540694  PubMed]
 
−
# Ali, N. O., J. Jeusset, E. Larquet, E. le Cam, B. Belitsky, A. L. Sonenshein, T. Msadek, and M. Débarbouillé. 2003. Specificity of the interaction of RocR with the ''rocG-rocA'' intergenic region in ''Bacillus subtilis''. Microbiology 149: 739-750. [http://www.ncbi.nlm.nih.gov/sites/entrez/12634342 PubMed]
 
−
# Calogero S, Gardan R, Glaser P, Schweizer J, Rapoport G, Debarbouille M. (1994) RocR, a novel regulatory protein controlling arginine utilization in ''Bacillus subtilis'', belongs to the NtrC/NifA family of transcriptional activators.  ''J. Bacteriol.'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/8113162 PubMed]
 
−
# Author1, Author2 & Author3 (year) Title # Author1, Author2 & Author3 (year) Title ''Journal'' '''176:''' 1234-1241. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 

Revision as of 16:52, 15 April 2009

  • Description: ornithine transaminase

Gene name rocD
Synonyms
Essential no
Product ornithine transaminase
Function arginine, ornithine and citrulline utilization
MW, pI 43 kDa, 4.894
Gene length, protein length 1203 bp, 401 aa
Immediate neighbours rocE, rocR
Hier soll was neues rein
Genetic context
RocD context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

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:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulatory mechanism: RocR: transcription activation PubMed
  • 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. Gardan R, Rapoport G, Débarbouillé M. (1995) Expression of the rocDEF operon involved in arginine catabolism in Bacillus subtilis. J Mol Biol. Jun 23;249(5): 843-56. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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