Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' Transcriptional antiterminator, controls expression of the ''ptsGHI'' operon<br/><br/>
+
* '''Description:''' glycogen phosphorylase <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'''
−
|''glcT''
+
|''glgP''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykwA''
+
|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 antiterminator of the ''ptsGHI'' operon
+
|style="background:#ABCDEF;" align="center"| '''Product''' || glycogen phosphorylase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || transcriptional antiterminator
+
|style="background:#ABCDEF;" align="center"|'''Function''' || glycogen biosynthesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33,0 kDa, 7.01
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 91 kDa, 6.28 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 855 bp, 285 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2394 bp, 798 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykvZ]]'', ''[[ptsG]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytaB]]'', ''[[glgA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13261&#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:CAB15072&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:glcT_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:glgP_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 ===
  
−
* '''Locus tag:''' BSU13880
+
* '''Locus tag:''' BSU30940
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 42: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/glgBCDAP.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12593]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10911]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' transcriptional antiterminator, RNA-binding protein, binds the ''[[ptsG]]'' RAT sequence
+
* '''Catalyzed reaction/ biological activity:''' (1,4-alpha-D-glucosyl)(n) + phosphate = (1,4-alpha-D-glucosyl)(n-1) + alpha-D-glucose 1-phosphate (according to Swiss-Prot)
  
−
* '''Protein family:''' antiterminator of the BglG/ [[SacY]] family
+
* '''Protein family:''' glycogen phosphorylase family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):''' [[LicT]], [[SacT]], [[SacY]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 63: Line 63:
  
 
* '''Domains:'''  
 
* '''Domains:'''  
−
** RNA-binding domain (N-terminal, constitutive antiterminator)
 
−
** 2x PTS regulation domains (PRDs) (C-terminal, neg. regulated by [[PtsG]])
 
  
−
* '''Modification:''' phosphorylation (His104)
+
* '''Modification:''' phosphorylation on (Thr-291 OR Ser-294) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 72: Line 70:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[PtsH]]-[[GlcT]]
+
* '''Interactions:'''
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 80: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31691]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39123 P39123]
 +
 
 +
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU30940]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU13880]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.4.1.1 2.4.1.1]
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=Expression and regulation=
 
=Expression and regulation=
Line 91: Line 90:
 
* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 101: Line 100:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP109 (in frame deletion), available in [[Stülke]] lab
+
* '''Mutant:'''
  
−
* '''Expression vector:''' pGP124 (full length, in [[pWH844]]), pGP114 (amino acids 1-60, RNA-binding domain, in [[pWH844]]), pGP230 (amino acids 1-60, RNA-binding domain with thrombin cleavage site, in [[pWH844]]), pGP164 (both PRDs, in [[pWH844]]), in addition diverse expression vectors for phosphorylation site mutants and for RBD mutants (all in [[pWH844]]), pGP424 (PRDI, in [[pWH844]]), pGP425 (PRDII, in [[pWH844]]), pGP442 (PRDI, in [[pGP570]], with thrombin cleavage site), pGP443 (PRDII, in [[pGP570]],  with thrombin cleavage site), pGP575 (amino acids 1-60, RNA-binding domain with Strep-tag, in [[pGP574]]), all available in [[Stülke]] lab
+
* '''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=
−
 
−
[[Stülke|Jörg Stülke]], University of Göttingen, Germany
 
−
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 120: Line 118:
 
=References=
 
=References=
  
−
<pubmed>11902727 9765562 12437213 10543968 17074746 15155854 14527945 9663674, </pubmed>
+
<pubmed>17218307, </pubmed>
−
# Stülke J, Martin-Verstraete I, Zagorec M (1997) Induction of the ''Bacillus subtilis ptsGHI'' operon by glucose is controlled by a novel antiterminator, ''GlcT Mol Microbiol.''  '''25:''' 65-78. [http://www.ncbi.nlm.nih.gov/sites/entrez/11902727 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]
−
# Bachem S, Stülke J. (1998)   Regulation of the ''Bacillus subtilis'' GlcT antiterminator protein by components of the phosphotransferase system. ''J Bacteriol.'' '''180:''' 5319-26 [http://www.ncbi.nlm.nih.gov/sites/entrez/9765562 PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Greenberg, D. B., Stülke, J. & Saier Jr., M. H. (2002) Domain analysis of transcriptional regulators bearing PTS-regulatory domains. Res. Microbiol. 153: 519-526. [http://www.ncbi.nlm.nih.gov/sites/entrez/12437213 PubMed]
 
−
# Langbein, I., Bachem, S. & Stülke, J. (1999) Specific interaction of the RNA binding domain of the Bacillus subtilis transcriptional antiterminator GlcT with its RNA target, RAT. J. Mol. Biol. 293: 795-805. [http://www.ncbi.nlm.nih.gov/sites/entrez/10543968 PubMed]
 
−
# Schilling, O., Herzberg, C., Hertrich, T., Vörsmann, H., Jessen, D., Hübner, S., Titgemeyer, F. & Stülke, J. (2006) Keeping signals straight in transcription regulation: specificity determinants for the interaction of a family of conserved bacterial RNA-protein couples. Nucl. Acids Res. 34: 6102-6115. [http://www.ncbi.nlm.nih.gov/sites/entrez/17074746 PubMed]
 
−
# Schilling, O., Langbein, I., Müller, M., Schmalisch, M. & Stülke, J. (2004) A protein-dependent riboswitch controlling ptsGHI operon expression in Bacillus subtilis: RNA structure rather than sequence provides interaction specificity. Nucl. Acids Res. 32: 2853-2864. [http://www.ncbi.nlm.nih.gov/sites/entrez/15155854 PubMed]
 
−
# Schmalisch, M., Bachem, S. & Stülke, J. (2003) Control of the Bacillus subtilis antiterminator protein GlcT by phosphorylation: Elucidation of the phosphorylation chain leading to inactivation of GlcT. J. Biol. Chem. 278: 51108-51115. [http://www.ncbi.nlm.nih.gov/sites/entrez/14527945 PubMed]
 
−
# Stülke, J., Arnaud, M., Rapoport, G., & Martin-Verstraete, I. (1998) PRD - A protein domain involved in PTS-dependent induction and carbon catabolite repression of catabolic operons in bacteria. Mol. Microbiol. 28: 865-874. [http://www.ncbi.nlm.nih.gov/sites/entrez/9663674 PubMed]
 

Revision as of 14:04, 8 June 2009

  • Description: glycogen phosphorylase

Gene name glgP
Synonyms
Essential no
Product glycogen phosphorylase
Function glycogen biosynthesis
MW, pI 91 kDa, 6.28
Gene length, protein length 2394 bp, 798 aa
Immediate neighbours ytaB, glgA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
GlgP context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU30940

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: (1,4-alpha-D-glucosyl)(n) + phosphate = (1,4-alpha-D-glucosyl)(n-1) + alpha-D-glucose 1-phosphate (according to Swiss-Prot)
  • Protein family: glycogen phosphorylase family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylation on (Thr-291 OR Ser-294) PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • KEGG entry: [3]

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
Retrieved from "https://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=89115"