Difference between revisions of "Sandbox"

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* '''Description:''' hydrolysis of 5-bromo-4-chloroindolyl phosphate <br/><br/>
+
* '''Description:''' xylan beta-1,4-xylosidase <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'''
|''xpaC''
+
|''xynB''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ynaK ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || xylan beta-1,4-xylosidase
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || xylan degradation
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 10.149  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61 kDa, 5.326  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 612 bp, 204 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1599 bp, 533 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[csfB]]'', ''[[yaaN]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[xynP]]'', ''[[xylR]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11801&#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:CAB13642&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:xpaC_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:xynB_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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__TOC__
 
__TOC__
  
<br/><br/>
+
<br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 35: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
* '''Locus tag:''' BSU00250
+
* '''Locus tag:''' BSU17580
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/xpaC-yaaN.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/xynPB.html]
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10089]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11987]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' Hydrolysis of (1->4)-beta-D-xylans, to remove successive D-xylose residues from the non-reducing termini (according to Swiss-Prot)
  
* '''Protein family:'''
+
* '''Protein family:''' glycosyl hydrolase 43 family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 72: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
* '''Localization:'''
+
* '''Localization:''' cell membrane (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
  
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1YIF 1YIF]
  
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P37467 P37467]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P94489 P94489]
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00250]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU17580]
  
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.2.1.37 3.2.1.37]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
* '''Operon:''' ''[[xpaC]]-[[yaaN]]''
+
* '''Operon:''' ''[[xynP]]-[[xynB]]''
  
* '''[[Sigma factor]]:''' [[SigW]] [http://www.ncbi.nlm.nih.gov/sites/entrez/9987136 PubMed]
+
* '''[[Sigma factor]]:''' [[SigA]]
  
* '''Regulation:''' expressed in stationary phase
+
* '''Regulation:''' repressed by glucose ([[CcpA]]) ,  carbon catabolite repression ([[CcpA]]), induction by xylose ([[XylR]])
  
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  [[CcpA]]: transcription repression, [[XylR]]: transcription repression
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 118: Line 120:
 
=References=
 
=References=
  
<pubmed>9987136, </pubmed>
+
<pubmed>8012596, </pubmed>
# Huang et al. (1999) Identification of target promoters for the Bacillus subtilis extracytoplasmic function [[sigma factor]], sigma W. ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
 
# Author1, Author2 & Author3 (year) Title ''Mol. Microbiol.'' '''31:''' 361-371. [http://www.ncbi.nlm.nih.gov/sites/entrez/9987136 PubMed]
+
# Lindner, C., Stülke, J. & Hecker, M. (1994) Regulation of xylanolytic enzymes in Bacillus subtilis. Microbiology 140: 753-757. [http://www.ncbi.nlm.nih.gov/sites/entrez/8012596 PubMed]
 +
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 13:41, 8 June 2009

  • Description: xylan beta-1,4-xylosidase

Gene name xynB
Synonyms ynaK
Essential no
Product xylan beta-1,4-xylosidase
Function xylan degradation
MW, pI 61 kDa, 5.326
Gene length, protein length 1599 bp, 533 aa
Immediate neighbours xynP, xylR
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
XynB context.gif
This image was kindly provided by SubtiList




The gene

Basic information

  • Locus tag: BSU17580

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Hydrolysis of (1->4)-beta-D-xylans, to remove successive D-xylose residues from the non-reducing termini (according to Swiss-Prot)
  • Protein family: glycosyl hydrolase 43 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: cell membrane (according to Swiss-Prot)

Database entries

  • KEGG entry: [3]

Additional information

Expression and regulation

  • Regulation: repressed by glucose (CcpA) , carbon catabolite repression (CcpA), induction by xylose (XylR)
  • Regulatory mechanism: CcpA: transcription repression, CcpA: transcription repression, XylR: transcription repression
  • 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

C Lindner, J Stülke, M Hecker
Regulation of xylanolytic enzymes in Bacillus subtilis.
Microbiology (Reading): 1994, 140 ( Pt 4);753-7
[PubMed:8012596] [WorldCat.org] [DOI] (P p)


  1. Lindner, C., Stülke, J. & Hecker, M. (1994) Regulation of xylanolytic enzymes in Bacillus subtilis. Microbiology 140: 753-757. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed