Difference between revisions of "Sandbox"

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* '''Description:''' transcriptional repressor of the xyl and xyn operons <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'''
−
|''xylR''
+
|''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  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional repressor
+
|style="background:#ABCDEF;" align="center"| '''Product''' || xylan beta-1,4-xylosidase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of xylan and xylose utilization
+
|style="background:#ABCDEF;" align="center"|'''Function''' || xylan degradation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 38 kDa, 5.819  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61 kDa, 5.326  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1050 bp, 350 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1599 bp, 533 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[xynB]]'', ''[[xylA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[xynP]]'', ''[[xylR]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
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|-
 
|-
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:xylR_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/><br/>
  
 
=The gene=
 
=The gene=
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/xylR.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/xynPB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11986]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11987]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' transcription repression of the ''[[xylA]]-[[xylB]]'' and the ''[[xynP]]-[[xynB]]'' operons
+
* '''Catalyzed reaction/ biological activity:'''  
  
 
* '''Protein family:'''
 
* '''Protein family:'''
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* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:''' inducer: xylose
+
* '''Effectors of protein activity:'''
  
 
* '''Interactions:'''
 
* '''Interactions:'''
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU17590]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU17580]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''xylR''
+
* '''Operon:''' ''[[xynP]]-[[xynB]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:'''  
+
* '''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:'''
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Wolfgang Hillen]], Erlangen University, Germany [http://www.biologie.uni-erlangen.de/mibi/index2.html Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 123: Line 121:
  
  
−
# Dahl, M. K., Schmiedel, D., and Hillen, W. (1995) Glucose and glucose-6-phosphate interaction with Xyl repressor proteins from Bacillus spp. may contribute to regulation of xylose utilization. J Bacteriol 177: 5467-5472. [http://www.ncbi.nlm.nih.gov/sites/entrez/7559331 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]
−
# Kauder C, Allmansberger R, Gärtner D, Schmiedel D, Hillen W. 1993. An operator binding-negative mutation of Xyl repressor from Bacillus subtilis is trans dominant in Bacillus megaterium. FEMS Microbiol. Lett. 109:81-84. [http://www.ncbi.nlm.nih.gov/sites/entrez/8319885 PubMed]
 
−
# Kreuzer P, Gärtner D, Allmansberger R, Hillen W. 1989. Identification and sequence analysis of the Bacillus subtilis W23 xylR gene and xyl operator. J. Bacteriol. 171:3840-3845. [http://www.ncbi.nlm.nih.gov/sites/entrez/2544559 PubMed]
 
−
# Gärtner D, Degenkolb J, Ripperger JAE, Allmansberger R, Hillen W. 1992. Regulation of the Bacillus subtilis W23 xylose utilization operon: interaction of Xyl repressor with xyl operator and the inducer xylose. Mol. Gen. Genet. 232:415-422 [http://www.ncbi.nlm.nih.gov/sites/entrez/1588910 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 15:21, 15 April 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
Hier soll was neues rein
Genetic context
XynB 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:

Database entries

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

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

  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
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