Difference between revisions of "Sandbox"

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−
* '''Description:''' endo-1,5-alpha-L-arabinosidase <br/><br/>
+
* '''Description:''' extracellular alkaline serine protease (subtilisin E) <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'''
−
|''abn2''
+
|''aprE''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxiA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''sprE ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || endo-1,5-alpha-L-arabinosidase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || extracellular alkaline serine protease (subtilisin E))
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || arabinan degradation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 7.371  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 39 kDa, 9.342  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1407 bp, 469 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1143 bp, 381 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxiB]]'', ''[[hutP]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhfN]]'', ''[[yhfO]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yxiA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/aprE_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yxiA_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/aprE_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:yxiA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:aprE_context.gif]]
 +
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
 
|}
 
|}
Line 43: Line 44:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yxiA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/aprE.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11130]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10190]
  
 
=== Additional information===
 
=== Additional information===
Line 62: Line 63:
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
  
−
* '''Kinetic information:''' With linear-alpha-1,5-l-arabinan as the preferred substrate, the enzyme exhibited an apparent K(m) of 2.0 mg ml(-1) and V(max) of 0.25 mmol min(-1) mg(-1) at pH 7.0 and 50°C. [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
+
* '''Kinetic information:'''
  
 
* '''Domains:'''  
 
* '''Domains:'''  
Line 74: Line 75:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed],  extracellular [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
+
* '''Localization:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:'''
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU10300]
  
−
* '''E.C. number:''' 3.2.1.99
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
Line 90: Line 91:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''abn2'' [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]], [[SigH]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
+
* '''Sigma factor:'''  
  
−
* '''Regulation:''' repressed by glucose (4.3-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  expression is stimulated by arabinose and pectin and repressed by glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  unknown [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:''' the mRNA is extremely stable (more than 25 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/11101663 PubMed]
  
 
=Biological materials =
 
=Biological materials =
Line 115: Line 116:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Isabel de Sa-Nogueira]], Lisboa, Portugal [http://www.itqb.unl.pt/research/biology/microbial-genetics homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
−
 
  
 
=References=
 
=References=
  
 
# 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]
 
# 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]
−
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
+
# Hambraeus, G., Persson, M. & Rutberg, B. (2000). The ''aprE'' leader is a determinant of extreme mRNA stability in ''Bacillus subtilis''. Microbiology 146, 3051-3059. [http://www.ncbi.nlm.nih.gov/sites/entrez/11101663 PubMed]
−
# Inácio JM, and de Sá-Nogueira I(2008) Characterization of ''abn2'' (''yxiA''), encoding a ''Bacillus subtilis'' GH43 arabinanase, Abn2, and its role in arabino-polysaccharide degradation.''J. Bacteriol.'' '''190:''' 4272-4280. [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
+
# Hambraeus, G., Karhumaa, K. & Rutberg, B. (2002). A 5' stem-loop and ribosome binding but not translation are important for the stability of ''Bacillus subtilis aprE'' leader mRNA. Microbiology 148, 1795-1803. [http://www.ncbi.nlm.nih.gov/sites/entrez/12055299 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 16:26, 6 April 2009

  • Description: extracellular alkaline serine protease (subtilisin E)

Gene name aprE
Synonyms sprE
Essential no
Product extracellular alkaline serine protease (subtilisin E))
Function protein degradation
MW, pI 39 kDa, 9.342
Gene length, protein length 1143 bp, 381 aa
Immediate neighbours yhfN, yhfO
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
AprE context.gif
This image was kindly provided by SubtiList



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: extracellular (signal peptide) PubMed

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • Regulation:
  • Regulatory mechanism:
  • Additional information: the mRNA is extremely stable (more than 25 min) PubMed

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

  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. Hambraeus, G., Persson, M. & Rutberg, B. (2000). The aprE leader is a determinant of extreme mRNA stability in Bacillus subtilis. Microbiology 146, 3051-3059. PubMed
  3. Hambraeus, G., Karhumaa, K. & Rutberg, B. (2002). A 5' stem-loop and ribosome binding but not translation are important for the stability of Bacillus subtilis aprE leader mRNA. Microbiology 148, 1795-1803. PubMed
  4. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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