Difference between revisions of "Sandbox"

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−
* '''Description:''' trigger enzyme: major glucose permease of the PTS, EIICBA(Glc) <br/><br/>
+
* '''Description:''' alpha-L-arabinofuranosidase <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''
+
|''abf2''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ptsX, crr''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''xsa ''
 
|-
 
|-
−
|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''' || alpha-L-arabinofuranosidase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || glucose transport and phosphorylation, control of [[GlcT]] activity
+
|style="background:#ABCDEF;" align="center"|'''Function''' || arabinan degradation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 75,3 kDa, 5.40
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 5.329 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2097 bp, 699 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1485 bp, 495 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glcT]]'', ''[[ptsH]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[trxA]]'', ''[[etfA]]''
 
|-
 
|-
−
|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/xsa_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/xsa_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" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ptsG_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:xsa_context.gif]]
 
|-
 
|-
 
|}
 
|}
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 1456496 - 1458592
+
* '''Coordinates:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ptsGHI.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/xsa.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10198]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11985]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 53: Line 54:
 
=== 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):'''
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=== Extended information on the protein ===
 
=== Extended information on the protein ===
  
−
* '''Kinetic Fips riecht nach faulen Eiern '''
+
* '''Kinetic information:'''
  
 
* '''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):'''
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* '''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 protein [http://www.ncbi.nlm.nih.gov/sites/entrez/18763711 NCBI]
+
* '''Localization:'''
  
 
=== 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:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13890]
+
* '''Swiss prot entry:'''
  
−
* '''E.C. number:''' [http://www.expasy.ch/cgi-bin/get-enzyme-entry?2.7.1.69]
+
* '''KEGG entry:'''
 +
 
 +
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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* '''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:''' induction by glucose
+
* '''Regulation:'''  
  
−
* '''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]
+
* '''Regulatory mechanism:'''  
−
* '''Additional Fips riecht nach faulen Eiern '''
+
 
 +
* '''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=
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=References=
 
=References=
  
−
# 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 17:54, 18 March 2009

  • Description: alpha-L-arabinofuranosidase

Gene name abf2
Synonyms xsa
Essential no
Product alpha-L-arabinofuranosidase
Function arabinan degradation
MW, pI 56 kDa, 5.329
Gene length, protein length 1485 bp, 495 aa
Immediate neighbours trxA, etfA
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
Xsa context.gif



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:
  • 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. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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