Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' trigger enzyme: major glucose permease of the PTS, EIICBA(Glc) <br/><br/>
+
* '''Description:''' similar to proline permease <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'''
−
|''ptsG''
+
|''yodF''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ptsX, crr''
+
|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''' || glucose-specific enzyme IICBA component
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || glucose transport and phosphorylation, control of [[GlcT]] activity
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 75,3 kDa, 5.40
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 53 kDa, 9.682 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2097 bp, 699 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1488 bp, 496 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glcT]]'', ''[[ptsH]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mhqE]]'', ''[[ctpA]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ptsG_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yodF_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ptsG_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yodF_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yodF_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ptsG_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 36:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 1456496 - 1458592
+
* '''Coordinates:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 44: Line 42:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ptsGHI.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10198]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13535]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 54: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' transport and phosphorylation of glucose, receives a phosphate from [[PtsH |HPr]] at the IIA domain (His-620), the phosphate group is then transferred to the IIB domain (Cys-461) an finally to the incoming glucose. In the absence of glucose, PtsG phosphorylates and thereby inactivates the transcriptional antiterminator [[GlcT]].
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' PTS enzyme II, glucose family
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 65: Line 64:
  
 
* '''Domains:'''  
 
* '''Domains:'''  
−
** 11x transmembrane domain (16–36, 89–109, 139–159, 180–200, 233–253, 283–303, 313–333, 338–358, 365–385, 388–408)
 
−
** PTS EIIC domain (  1-424)
 
−
** PTS EIIB domain (439–520)
 
−
** PTS EIIA domain (568–672)
 
  
−
* '''Modification:''' transient  phosphorylation ([[PtsH |HPr]]-dependent) on His-620, then internal phosphotransfer from His-620 to Cys-461
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 76: Line 71:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' PtsG-[[PtsH |HPr]], PtsG-[[GlcT]] (for phosphorylation of [[GlcT]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14527945 PubMed]
+
* '''Interactions:'''
  
−
* '''Localization:''' membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed] ,  membrane protein [http://www.ncbi.nlm.nih.gov/sites/entrez/18763711 NCBI]
+
* '''Localization:''' membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]  
  
 
=== Database entries ===
 
=== Database entries ===
−
 
−
* '''Structure:''' IIA domain [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=56258 NCBI], NMR IIA domain [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=55395 NCBI]
 
  
−
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P20166]
+
* '''Structure:'''
 +
 
 +
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU13890]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU19580]
  
−
* '''E.C. number:''' [http://www.expasy.ch/cgi-bin/get-enzyme-entry?2.7.1.69]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
Line 95: Line 90:
  
 
* '''Operon:'''  
 
* '''Operon:'''  
−
**''[[ptsG]]-[[ptsH]]-[[ptsI]]''
 
−
**''[[ptsH]]-[[ptsI]]''
 
  
−
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11902727 PubMed]
+
* '''Sigma factor:'''  
 +
 
 +
* '''Regulation:'''
  
−
* '''Regulation:''' induction by glucose
+
* '''Regulatory mechanism:'''  
  
−
* '''Regulatory mechanism:''' transcriptional antitermination via the [[GlcT]]-dependent RNA-switch [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+9765562 PubMed]
+
* '''Additional information:'''  
−
* '''Additional information:'''
 
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP474 (cat), QB5436 (spc), QB5445 (erm), available in [[Stülke]] lab
+
* '''Mutant:'''
  
−
* '''Expression vector:''' pGP123 (domains BA, in [[pWH844]]), pGP123 (domains BA, mut: H620D, in [[pWH844]]), pGP428 (EIIB, in [[pWH844]]), pGP437(EIIA in [[pWH844]], with thrombin cleavage site), available in [[Stülke]] lab
+
* '''Expression vector:'''
−
+
       
−
* '''lacZ fusion:''' pGP34 ([[pAC5]]), pGP66 ([[pAC7]]), pGP606 (mutant terminator, [[pAC6]]), pGP532 ([[pAC7]]), series of promoter deletions are available in [[pAC5]] and [[pAC6]], series of RAT mutants are available in [[pAC6]], available in [[Stülke]] lab
+
* '''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 127: Line 120:
  
 
# 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]
 
# 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]
−
# 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]
 
−
# 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]
 
−
# Bachem, S., Faires, N., & Stülke, J. (1997) Characterization of the presumptive phosphorylation sites of the ''Bacillus subtilis'' glucose permease by site-directed mutagenesis: Implication in glucose transport and catabolite repression. FEMS Microbiol. L. 156: 233-238. [http://www.ncbi.nlm.nih.gov/sites/entrez/9513271 PubMed]
 
−
# Gonzy-Tréboul, G., de Waard, J. H., Zagorec, M., and Postma, P.W. (1991). The glucose permease of the phosphotransferase system of ''Bacillus subtilis'': Evidence for IIGlc and IIIGlc domains. Mol. Microbiol. 5, 1241-1249. [http://www.ncbi.nlm.nih.gov/sites/entrez/1956301 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]
 
−
# Zagorec, M. & Postma, P. (1992). Cloning and nucleotide sequence of the ''ptsG'' gene of ''Bacillus subtilis''. Mol Gen Genet 234, 325-328. [http://www.ncbi.nlm.nih.gov/sites/entrez/1508157 PubMed]
 
−
# Sutrina, S. L., Reddy, P., Saier, M. H., Jr & Reizer, J. (1990). The glucose permease of ''Bacillus subtilis'' is a single polypeptide chain that functions to energize the sucrose permease. J Biol Chem 265, 18581-18589. [http://www.ncbi.nlm.nih.gov/sites/entrez/2120236 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 15:04, 25 March 2009

  • Description: similar to proline permease

Gene name yodF
Synonyms
Essential no
Product unknown
Function unknown
MW, pI 53 kDa, 9.682
Gene length, protein length 1488 bp, 496 aa
Immediate neighbours mhqE, ctpA
Gene sequence (+200bp) Protein sequence
Genetic context
YodF 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:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: membrane PubMed

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [2]
  • E.C. number:

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

Your additional remarks

References

  1. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=44559"