Difference between revisions of "Sandbox"

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−
* '''Description:''' transcriptional regulator of transition state genes <br/><br/>
+
* '''Description:''' endo-1,5-alpha-L-arabinosidase <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'''
−
|''abh''
+
|''abn2''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ylxT, yzaA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxiA ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
+
|style="background:#ABCDEF;" align="center"| '''Product''' || endo-1,5-alpha-L-arabinosidase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of gene expression during the transition from growth to stationary phase
+
|style="background:#ABCDEF;" align="center"|'''Function''' || arabinan degradation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 10 kDa, 5.753  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 7.371  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 276 bp, 92 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1407 bp, 469 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mreBH]]'', ''[[kinC]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxiB]]'', ''[[hutP]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/abh_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|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/abh_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yxiA_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:abh_context.gif]]
+
|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]]
 
|-
 
|-
 
|}
 
|}
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/abh.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yxiA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10988]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11130]
  
 
=== Additional information===
 
=== Additional information===
Line 56: Line 58:
 
* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[AbrB]], [[SpoVT]] (only N-terminal domain)
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
  
−
* '''Kinetic information:'''
+
* '''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]
  
 
* '''Domains:'''  
 
* '''Domains:'''  
Line 72: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' extracellular [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''KEGG entry:'''
 
* '''KEGG entry:'''
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' 3.2.1.99
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[abh]]''
+
* '''Operon:''' ''abn2'' [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
  
−
* '''Sigma factor:''' [[SigW]], [[SigX]]
+
* '''Sigma factor:''' [[SigA]], [[SigH]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' expression is stimulated by arabinose and pectin and repressed by glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' unknown [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 114: Line 116:
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
  
−
[[Mark Strauch]], Baltimore, USA [http://lifesciences.umaryland.edu/Pages/faculty_profile.aspx?ID=212 homepage]
+
[[Isabel de Sa-Nogueira]], Lisboa, Portugal [http://www.itqb.unl.pt/research/biology/microbial-genetics homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
 +
  
 
=References=
 
=References=
  
−
# Yao, F and M.A. Strauch (2005) Independent and Interchangeable Multimerization Domains of the AbrB, Abh and SpoVT Global Regulatory Proteins. J. Bacteriol. 187:6354-6362 [http://www.ncbi.nlm.nih.gov/sites/entrez/16159768 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]
−
# Bobay, B.G., Mueller, G.A., Thompson, R.J., Venters, R.A., Murzin, A.G., Strauch, M.A. & J. Cavanagh (2006) NMR structure of AbhN and comparison with AbrBN: First Insights into the DNA-binding Promiscuity and Specificity of AbrB-like Transition-state Regulator Proteins. J. Biol. Chem. 281:21399-21409  [http://www.ncbi.nlm.nih.gov/sites/entrez/16702211 PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Strauch MA. Bobay BG. Cavanagh J. Yao F. Wilson A. Le Breton Y. (2007) Abh and AbrB control of Bacillus subtilis antimicrobial gene expression. J. of Bacteriol. 189:7720-7732. [http://www.ncbi.nlm.nih.gov/sites/entrez/17720793 PubMed]
 

Revision as of 17:55, 18 March 2009

  • Description: endo-1,5-alpha-L-arabinosidase

Gene name abn2
Synonyms yxiA
Essential no
Product endo-1,5-alpha-L-arabinosidase
Function arabinan degradation
MW, pI 52 kDa, 7.371
Gene length, protein length 1407 bp, 469 aa
Immediate neighbours yxiB, hutP
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
YxiA 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: 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. PubMed
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: extracellular PubMed

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry:
  • E.C. number: 3.2.1.99

Additional information

Expression and regulation

  • Regulation: expression is stimulated by arabinose and pectin and repressed by glucose PubMed
  • Regulatory mechanism: unknown PubMed
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Isabel de Sa-Nogueira, Lisboa, Portugal homepage

Your additional remarks

References

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