Difference between revisions of "Sandbox"

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−
* '''Description:''' probable regulator of transcription of SigF-dependent genes <br/><br/>
+
* '''Description:''' levansucrase <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'''
−
|''rsfA''
+
|''sacB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywfN, ipa-92r ''
+
|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''' || regulator of SigF activity
+
|style="background:#ABCDEF;" align="center"| '''Product''' || levansucrase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || control of expression of SigF-dependent genes
+
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of sucrose, production of levan
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.13  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 6.175  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 774 bp, 258 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1419 bp, 473 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywzC]]'', ''[[ywfM]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pbpE]]'', ''[[levB]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15789&#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:CAB15450&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:rsfA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:sacB_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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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU37620
+
* '''Locus tag:''' BSU34450
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rsfA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sacB-yveBA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10638]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10388]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' Sucrose + (6)-beta-D-fructofuranosyl-(2->)(n) alpha-D-glucopyranoside = glucose + (6)-beta-D-fructofuranosyl-(2->)(n+1) alpha-D-glucopyranoside (according to Swiss-Prot)
  
−
* '''Protein family:'''
+
* '''Protein family:''' glycosyl hydrolase 68 family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' forespore (according to Swiss-Prot)
+
* '''Localization:''' secreted (according to Swiss-Prot),  extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1PT2 1PT2] (complex with sucrose),  [http://www.rcsb.org/pdb/explore.do?structureId=1OYG 1OYG]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39650 P39650]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P05655 P05655]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37620]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU34450]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.4.1.10 2.4.1.10]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''rsfA''
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:''' repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed] 
+
* '''Regulation:''' induction by sucrose (at high concentration)
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' induction by [[SacY]]-dependent RNA switch (transcriptional antitermination), in addition activated by [[DegU]]-P
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 118: Line 118:
 
=References=
 
=References=
  
−
<pubmed>12107147, </pubmed>
+
<pubmed>18957862 2105292, </pubmed>
−
# M&#228;der et al. (2002) Transcriptome and Proteome Analysis of ''Bacillus subtilis'' Gene Expression Modulated by Amino Acid Availability. ''J. Bacteriol'' '''184:''' 1844288-4295 [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
+
# Voigt et al. (2009) Cell physiology and protein secretion of ''Bacillus licheniformis'' compared to ''Bacillus subtilis''. ''J Mol Microbiol Biotechnol.'' '''16:''' 53-68 [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
 +
# Crutz AM, Steinmetz M, Aymerich S, Richter R, Le Coq D (1990) Induction of levansucrase in Bacillus subtilis: an antitermination mechanism negatively controlled by the phosphotransferase system. J Bacteriol 172:1043-1050. [http://www.ncbi.nlm.nih.gov/sites/entrez/2105292 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 13:35, 8 June 2009

  • Description: levansucrase

Gene name sacB
Synonyms
Essential no
Product levansucrase
Function utilization of sucrose, production of levan
MW, pI 52 kDa, 6.175
Gene length, protein length 1419 bp, 473 aa
Immediate neighbours pbpE, levB
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
SacB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU34450

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Sucrose + (6)-beta-D-fructofuranosyl-(2->)(n) alpha-D-glucopyranoside = glucose + (6)-beta-D-fructofuranosyl-(2->)(n+1) alpha-D-glucopyranoside (according to Swiss-Prot)
  • Protein family: glycosyl hydrolase 68 family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: secreted (according to Swiss-Prot), extracellular (signal peptide) PubMed

Database entries

  • Structure: 1PT2 (complex with sucrose), 1OYG
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Operon:
  • Regulation: induction by sucrose (at high concentration)
  • Regulatory mechanism: induction by SacY-dependent RNA switch (transcriptional antitermination), in addition activated by DegU-P
  • 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

Birgit Voigt, Haike Antelmann, Dirk Albrecht, Armin Ehrenreich, Karl-Heinz Maurer, Stefan Evers, Gerhard Gottschalk, Jan Maarten van Dijl, Thomas Schweder, Michael Hecker
Cell physiology and protein secretion of Bacillus licheniformis compared to Bacillus subtilis.
J Mol Microbiol Biotechnol: 2009, 16(1-2);53-68
[PubMed:18957862] [WorldCat.org] [DOI] (I p)

A M Crutz, M Steinmetz, S Aymerich, R Richter, D Le Coq
Induction of levansucrase in Bacillus subtilis: an antitermination mechanism negatively controlled by the phosphotransferase system.
J Bacteriol: 1990, 172(2);1043-50
[PubMed:2105292] [WorldCat.org] [DOI] (P p)

  1. Voigt et al. (2009) Cell physiology and protein secretion of Bacillus licheniformis compared to Bacillus subtilis. J Mol Microbiol Biotechnol. 16: 53-68 PubMed
  2. Crutz AM, Steinmetz M, Aymerich S, Richter R, Le Coq D (1990) Induction of levansucrase in Bacillus subtilis: an antitermination mechanism negatively controlled by the phosphotransferase system. J Bacteriol 172:1043-1050. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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