Difference between revisions of "Sandbox"

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* '''Description:''' transcriptional antiterminator of the ''bglPH'' operon<br/><br/>
+
* '''Description:''' secondary transporter of divalent metal ions/citrate complexes <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'''
−
|''licT''
+
|''citH''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxiQ ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional antiterminator (BglG family)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || secondary transporter of divalent metal ions/citrate complexes
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || required for substrate-dependent induction of ''bglPH''
+
|style="background:#ABCDEF;" align="center"|'''Function''' || citrate  uptake
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 32 kDa, 5.944  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 9.278  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 831 bp, 277 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1278 bp, 426 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[bglS]]'', ''[[yxiP]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[katE]]'', ''[[bglS]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15944&#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:CAB15932&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
 
|-
 
|-
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:licT_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:citH_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=
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===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
no expression of the ''[[bglP]]-[[bglH]]'' operon
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/licT-bglS.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10474]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11146]
  
 
=== Additional information===
 
=== Additional information===
Line 56: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' binding to the mRNAs of ''[[bglS]]'' and the ''[[bglP]]-[[bglH]]'' operon, causes transcription antitermination (in presence of salicin and absence of glucose)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' BglG family of antiterminators
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[SacY]], [[GlcT]], [[SacT]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylation on Ser-149 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU39080]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU39060]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 92: Line 90:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[licT]]-[[bglS]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8606172 PubMed]
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/8606172 PubMed]
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 100: Line 98:
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 117: Line 115:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France
 
−
 
−
[[Josef Deutscher]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France
 
−
 
−
[[Michael Hecker]], Greifswald, Germany [http://www.mikrobiologie.uni-greifswald.de/index.php?id=20 Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
'''Original description'''
+
# 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]
−
# Schnetz, K., Stülke, J., Gertz, S., Krüger, S., Krieg, M., Hecker, M. & Rak, B. (1996) LicT, a Bacillus subtilis transcriptional antiterminator protein of the BglG family. J. Bacteriol. 178: 1971-1979. [http://www.ncbi.nlm.nih.gov/sites/entrez/8606172 PubMed]
 
−
 
 
−
'''Control of LicT activity'''
 
−
# Lindner, C., Galinier, A., Hecker, M. & Deutscher, J. (1999) Regulation of the activity of the Bacillus subtilis antiterminator LicT by multiple PEP-dependent, enzyme I- and HPr-catalysed phosphorylation. Mol. Microbiol. 31, 995-1006 . [http://www.ncbi.nlm.nih.gov/sites/entrez/10048041  PubMed]
 
−
# Lindner, C., Hecker, M., Le Coq, D. & Deutscher, J. (2002) Bacillus subtilis mutant LicT antiterminators exhibiting enzyme I- and HPr-independent antitermination affect catabolite repression of the bglPH operon. J. Bacteriol. 184, 4819-4828 . [http://www.ncbi.nlm.nih.gov/sites/entrez/12169607  PubMed]
 
−
# Krüger, S., Gertz, S. & Hecker, M. Transcriptional analysis of bglPH expression in Bacillus subtilis: Evidence for two distinct pathways mediating carbon catabolite repression. J. Bacteriol. 178, 2637-2644 (1996). [http://www.ncbi.nlm.nih.gov/sites/entrez/8626332 PubMed]
 
−
# Tortosa, P., Declerck, N., Dutartre, H., Lindner, C., Deutscher, J., and Le Coq, D. (2001) Sites of positive and negative regulation in the Bacillus subtilis antiterminators LicT and SacY. Mol Microbiol 41: 1381-1393. [http://www.ncbi.nlm.nih.gov/sites/entrez/11580842 PubMed]
 
−
 
 
−
'''Structural analysis of LicT'''
 
−
# Declerck N, Dutartre H, Receveur V, Dubois V, Royer C, Aymerich S, van Tilbeurgh H (2001) Dimer stabilization upon activation of the transcriptional antiterminator LicT. J Mol Biol 314:671-681. [http://www.ncbi.nlm.nih.gov/sites/entrez/11733988 PubMed]
 
−
# Graille, M. et al. Activation of the LicT transcriptional antiterminator involves a domain swing/lock mechanism provoking massive structural changes. J. Biol. Chem. 280, 14780-14789 (2005). [http://www.ncbi.nlm.nih.gov/sites/entrez/15699035 PubMed]
 
−
# van Tilbeurgh H, Le Coq D, Declerck N (2001) Crystal structure of an activated form of the PTS regulation domain from the LicT transcriptional antiterminator. EMBO J 20:3789-3799. [http://www.ncbi.nlm.nih.gov/sites/entrez/11447120 PubMed]
 
−
# Déméné H, Ducat T, De Guillen K, Birck C, Aymerich S, Kochoyan M, Declerck N.(2008) Structural mechanism of signal transduction between the RNA-binding domain and the phosphotransferase system regulation domain of the LicT antiterminator.''J. Biol. Chem.'' '''283:''' 30838-30849. [http://www.ncbi.nlm.nih.gov/sites/entrez/18682383 PubMed]
 
−
 
 
−
'''LicT-RNA interaction'''
 
−
# Yang Y, Declerck N, Manival X, Aymerich S, Kochoyan M (2002) Solution structure of the LicT-RNA antitermination complex: CAT clamping RAT. EMBO J 21:1987-1997. [http://www.ncbi.nlm.nih.gov/sites/entrez/11953318 PubMed]
 
−
# Aymerich, S. and Steinmetz, M. (1992) Specificity determinants and structural features in the RNA target of the bacterial antiterminator proteins of the BglG/SacY family. Proc. Natl. Acad. Sci. USA 89, 10410-10414. [http://www.ncbi.nlm.nih.gov/sites/entrez/1279678 PubMed]
 
−
# Declerck, N., Vincent, F., Hoh, F., Aymerich, S. and van Tilbeurgh, H. (1999) RNA recognition by transcriptional antiterminators of the BglG/SacY family: functional and structural comparison of the CAT domains from SacY and LicT. J. Mol. Biol. 294, 389-402. [http://www.ncbi.nlm.nih.gov/sites/entrez/10610766 PubMed]
 
−
# Déméné H, Ducat T, De Guillen K, Birck C, Aymerich S, Kochoyan M, Declerck N.(2008) Structural mechanism of signal transduction between the RNA-binding domain and the phosphotransferase system regulation domain of the LicT antiterminator.''J. Biol. Chem.'' '''283:''' 30838-30849. [http://www.ncbi.nlm.nih.gov/sites/entrez/18682383 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 23:52, 16 April 2009

  • Description: secondary transporter of divalent metal ions/citrate complexes

Gene name citH
Synonyms yxiQ
Essential no
Product secondary transporter of divalent metal ions/citrate complexes
Function citrate uptake
MW, pI 45 kDa, 9.278
Gene length, protein length 1278 bp, 426 aa
Immediate neighbours katE, bglS
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
CitH 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: phosphorylation on Ser-149 PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

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. Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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