Difference between revisions of "Sandbox"

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* '''Description:''' glutamine synthetase <br/><br/>
+
* '''Description:''' xylose isomerase <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'''
−
|''glnA''
+
|''xylA''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || trigger enzyme: glutamine synthetase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || xylose isomerase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || glutamine biosynthesis, control of TnrA and GlnR activity
+
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of xylan and xylose
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 4.874  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 5.635  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1332 bp, 444 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1335 bp, 445 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glnR]]'', ''[[ynxB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[xylR]]'', ''[[xylB]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13630&#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:CAB13644&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:glnA_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:xylA_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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===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
auxotrophic for glutamine
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/glnRA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/xylAB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10425]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10806]
  
 
=== Additional information===
 
=== Additional information===
Line 62: Line 62:
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
  
−
* '''Kinetic information:''' K(M) for: Glu: 27 mM, ATP: 2.4 mM, ammonium: 0.18 mM; v(max): 3.7 µmol/min/mg
+
* '''Kinetic information:'''
  
−
* '''Domains:''' glutamate binding flap (aa 300 ... 306: protects unstable intermediates from abberant hydrolysis)
+
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
+
* '''Modification:'''
  
−
* '''Cofactor(s):''' Mg(2+)
+
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:''' feedback inhibition by glutamine, glutamine binds thhe entrance site for glutamate
+
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[TnrA]]-[[GlnA]],  [[GlnR]]-[[GlnA]], (only the feedback-inhibited enzyme interacts with [[TnrA]] and [[GlnR]])
+
* '''Interactions:'''
  
 
* '''Localization:''' Cytoplasm
 
* '''Localization:''' Cytoplasm
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU17460]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU17600]
−
 
 
−
* '''E.C. number:''' 6.3.1.2
 
  
 +
* '''E.C. number:''' 5.3.1.5
  
 
=== Additional information===
 
=== Additional information===
−
 
−
GlnA is a homooligomer of 12 subunits
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[glnR]]-[[glnA]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8636055 PubMed]
+
* '''Operon:''' ''[[xylA]]-[[xylB]]''
  
 
* '''[[Sigma factor]]:''' [[SigA]]
 
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:''' expressed in the absence of glutamine [http://www.ncbi.nlm.nih.gov/sites/entrez/8636055 PubMed]
+
* '''Regulation:''' repressed by glucose ([[CcpA]]) ,  carbon catabolite repression ([[CcpA]]), induction by xylose ([[XylR]])
  
−
* '''Regulatory mechanism:''' repressed by [[GlnR]]-[[GlnA]] complex [http://www.ncbi.nlm.nih.gov/sites/entrez/8636055 PubMed]
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  [[CcpA]]: transcription repression, [[XylR]]: transcription repression
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 115: Line 112:
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
  
−
* '''Antibody:''' available in [[Karl Forchhammer]] lab
+
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
  
−
[[Susan Fisher]], Boston, USA [http://www.bumc.bu.edu/microbiology/research/susan-h-fisher-phd/ homepage]
+
[[Wolfgang Hillen]], Erlangen University, Germany [http://www.biologie.uni-erlangen.de/mibi/index2.html Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 125: Line 122:
 
=References=
 
=References=
  
−
# L&#233;vine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. ''Proteomics'' '''6:''' 2157-2173 [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
+
 
−
# Brown, S. W., and A. L. Sonenshein. 1996. Autogenous regulation of the ''Bacillus subtilis glnRA'' operon. J. Bacteriol. 178: 2450-2454. [http://www.ncbi.nlm.nih.gov/sites/entrez/8636055 PubMed]
+
# Dahl, M. K., J. Degenkolb, and W. Hillen. 1994. Transcription of the xyl operon is controlled in Bacillus subtilis by tandem overlapping operators spaced by four base-pairs. J. Mol. Biol. 243:413-424. [http://www.ncbi.nlm.nih.gov/sites/entrez/7966270 PubMed]
−
# Wray LV Jr, Zalieckas JM, Fisher SH. (2001) ''Bacillus subtilis'' glutamine synthetase controls gene expression through protein-protein interaction with transcription factor TnrA. Cell 107:427-435. [http://www.ncbi.nlm.nih.gov/sites/entrez/11719184 PubMed]
+
# Jacob S, Allmansberger R, Gärtner D, Hillen W (1991) Catabolite repression of the operon for xylose utilization from Bacillus subtilis W23 is mediated at the level of transcription and depends on a cis site in the xylA reading frame. Mol Gen Genet 229: 189-196. [http://www.ncbi.nlm.nih.gov/sites/entrez/1921970 PubMed]
−
# Fisher, S. H., and Wray, L. V., Jr. (2006) Feedback-resistant mutations in ''Bacillus subtilis'' glutamine synthetase are clustered in the active site. J Bacteriol 188: 5966-5974. [http://www.ncbi.nlm.nih.gov/sites/entrez/16885465 PubMed]
+
# Kraus A, Hueck C, Gärtner D, Hillen W (1994) Catabolite repression of the Bacillus subtilis xyl operon involves a cis element functional in the context of an unrelated sequence, and glucose exerts additional xylR-dependent repression. J Bacteriol 176: 1738-1745. [http://www.ncbi.nlm.nih.gov/sites/entrez/8132469 PubMed]
−
# Fisher SH, Sonenshein AL (1984) ''Bacillus subtilis'' glutamine synthetase mutants pleiotropically altered in catabolite repression. J Bacteriol 157:612-621. [http://www.ncbi.nlm.nih.gov/sites/entrez/6141156 PubMed]
+
# Gärtner D, Geißendörfer M, Hillen W. 1988. Expression of the Bacillus subtilis xyl operon is repressed at the level of transcription and is induced by xylose. J. Bacteriol. 170:3102-3109. [http://www.ncbi.nlm.nih.gov/sites/entrez/2454911 PubMed]
−
# Fisher, S. H., Brandenburg, J. L. & Wray, L. V. (2002). Mutations in ''Bacillus subtilis'' glutamine synthetase that block its interaction with transcription factor TnrA. Mol Microbiol 45, 627-635. [http://www.ncbi.nlm.nih.gov/sites/entrez/12139611 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]
−
# Schreier, H. J., Brown, S. W., Hirschi, K. D., Nomellini, J. F. & Sonenshein, A. L. (1989). Regulation of ''Bacillus subtilis'' glutamine synthetase gene expression by the product of the ''glnR'' gene. J Mol Biol 210, 51-63. [http://www.ncbi.nlm.nih.gov/sites/entrez/2573733 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 02:24, 30 April 2009

  • Description: xylose isomerase

Gene name xylA
Synonyms
Essential no
Product xylose isomerase
Function utilization of xylan and xylose
MW, pI 50 kDa, 5.635
Gene length, protein length 1335 bp, 445 aa
Immediate neighbours xylR, xylB
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
XylA 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: Cytoplasm

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number: 5.3.1.5

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

Wolfgang Hillen, Erlangen University, Germany Homepage

Your additional remarks

References

  1. Dahl, M. K., J. Degenkolb, and W. Hillen. 1994. Transcription of the xyl operon is controlled in Bacillus subtilis by tandem overlapping operators spaced by four base-pairs. J. Mol. Biol. 243:413-424. PubMed
  2. Jacob S, Allmansberger R, Gärtner D, Hillen W (1991) Catabolite repression of the operon for xylose utilization from Bacillus subtilis W23 is mediated at the level of transcription and depends on a cis site in the xylA reading frame. Mol Gen Genet 229: 189-196. PubMed
  3. Kraus A, Hueck C, Gärtner D, Hillen W (1994) Catabolite repression of the Bacillus subtilis xyl operon involves a cis element functional in the context of an unrelated sequence, and glucose exerts additional xylR-dependent repression. J Bacteriol 176: 1738-1745. PubMed
  4. Gärtner D, Geißendörfer M, Hillen W. 1988. Expression of the Bacillus subtilis xyl operon is repressed at the level of transcription and is induced by xylose. J. Bacteriol. 170:3102-3109. PubMed
  5. 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 PubMed
  6. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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