Difference between revisions of "Sandbox"

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−
* '''Description:''' non-specific DNA-binding protein Hbsu <br/><br/>
+
* '''Description:''' tryptophan operon RNA-binding attenuation protein (TRAP) <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'''
−
|''hbs''
+
|''mtrB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dbpA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || non-specific DNA-binding protein Hbsu
+
|style="background:#ABCDEF;" align="center"| '''Product''' || tryptophan operon RNA-binding attenuation protein (TRAP)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || DNA packaging, function of the signal recognition complex
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of tryptophan biosynthesis
 +
(and translation) attenuation in the trp operon);
 +
repression of the folate operon
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 9 kDa, 9.501  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 8 kDa, 7.333  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 276 bp, 92 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 225 bp, 75 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mtrA]]'', ''[[spoIVA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[hepS]]'', ''[[mtrA]]''
 
|-
 
|-
 
|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:hbs_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:mtrB_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 40:
  
 
===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/hbs.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/mtrAB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10276]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10278]
  
 
=== Additional information===
 
=== Additional information===
Line 66: Line 66:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylation on Thr-4 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 74: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
Line 82: Line 82:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU22790]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU22770]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 98: Line 98:
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:''' mRNA is protected from degradation by [[RnjA]] by initiating ribosomes [http://www.ncbi.nlm.nih.gov/sites/entrez/19210617 PubMed]
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 115: Line 115:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Ciaran Condon]], IBPC, Paris, France [http://www.ibpc.fr/UPR9073/condon/index_en.html Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 122: Line 120:
 
=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]
+
# Antson AA, Otridge J, Brzozowski AM, Dodson EJ, Dodson GG, Wilson KS, Smith TM, Yang M, Kurecki T, Gollnick P (1995) The structure of ''trp'' RNA-binding protein. Nature 374:693-700. [http://www.ncbi.nlm.nih.gov/sites/entrez/7715723 PubMed]
−
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707  [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
+
# Antson AA, Dodson EJ, Dodson G, Greaves RB, Chen XP, Gollnick P (1999) Structure of the ''trp'' RNA-binding attenuation protein, TRAP, bound to RNA. Nature 401:235-242. [http://www.ncbi.nlm.nih.gov/sites/entrez/10499579 PubMed]
−
# Daou-Chabo R, Mathy N, Bénard L, Condon C. (2009) Ribosomes initiating translation of the ''hbs'' mRNA protect it from 5'-to-3' exoribonucleolytic degradation by RNase J1.  ''Mol. Microbiol.'' '''71:''' 1538-1550. [http://www.ncbi.nlm.nih.gov/sites/entrez/19210617 PubMed]
+
# Babitzke P, Gollnick P (2001) Posttransription iniation control of tryptophan metabolism in ''Bacillus subtilis'' by the trp RNA-binding attenuation protein (TRAP), anti-TRAP, and RNA structure. J Bacteriol 183:5795-5802. [http://www.ncbi.nlm.nih.gov/sites/entrez/11566976 PubMed]
 +
# Babitzke P, Stults JT, Shire SJ, Yanofsky C (1994) TRAP, the trp RNA-binding attenuation protein of ''Bacillus subtilis'', is a multisubunit complex that appears  to recognize G/UAG repeats in the ''trpEDCFBA'' and ''trpG'' transcripts. J Biol Chem 269:16597-16604. [http://www.ncbi.nlm.nih.gov/sites/entrez/7515880 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 18:59, 15 April 2009

  • Description: tryptophan operon RNA-binding attenuation protein (TRAP)

Gene name mtrB
Synonyms
Essential no
Product tryptophan operon RNA-binding attenuation protein (TRAP)
Function regulation of tryptophan biosynthesis

(and translation) attenuation in the trp operon); repression of the folate operon

MW, pI 8 kDa, 7.333
Gene length, protein length 225 bp, 75 aa
Immediate neighbours hepS, mtrA
Hier soll was neues rein
Genetic context
MtrB 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

  • 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. Antson AA, Otridge J, Brzozowski AM, Dodson EJ, Dodson GG, Wilson KS, Smith TM, Yang M, Kurecki T, Gollnick P (1995) The structure of trp RNA-binding protein. Nature 374:693-700. PubMed
  2. Antson AA, Dodson EJ, Dodson G, Greaves RB, Chen XP, Gollnick P (1999) Structure of the trp RNA-binding attenuation protein, TRAP, bound to RNA. Nature 401:235-242. PubMed
  3. Babitzke P, Gollnick P (2001) Posttransription iniation control of tryptophan metabolism in Bacillus subtilis by the trp RNA-binding attenuation protein (TRAP), anti-TRAP, and RNA structure. J Bacteriol 183:5795-5802. PubMed
  4. Babitzke P, Stults JT, Shire SJ, Yanofsky C (1994) TRAP, the trp RNA-binding attenuation protein of Bacillus subtilis, is a multisubunit complex that appears to recognize G/UAG repeats in the trpEDCFBA and trpG transcripts. J Biol Chem 269:16597-16604. PubMed
  5. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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