Difference between revisions of "Sandbox"

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−
* '''Description:''' glutamine synthetase <br/><br/>
+
* '''Description:''' transketolase <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''
+
|''tkt''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''tktA ''
 
|-
 
|-
 
|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''' || transketolase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || glutamine biosynthesis, control of TnrA and GlnR activity
+
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 4.874  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 72 kDa, 4.803  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1332 bp, 444 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2001 bp, 667 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glnR]]'', ''[[ynxB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ynzC]]'', ''[[yneE]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/glnA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/tkt_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/glnA_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/tkt_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:glnA_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:tkt_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>
 
|-
 
|-
Line 39: Line 41:
  
 
===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/tkt.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10425]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11247]
  
 
=== Additional information===
 
=== Additional information===
Line 63: Line 63:
 
=== 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:''' phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]  
  
−
* '''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:''' [[GlnR]]-[[GlnA]], [[GlnA]]-[[TnrA]] (only the feedback-inhibited enzyme interacts with [[TnrA]] and [[GlnR]])
+
* '''Interactions:'''
  
 
* '''Localization:'''
 
* '''Localization:'''
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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+BSU17890]
−
 
 
−
* '''E.C. number:''' 6.3.1.2
 
  
 +
* '''E.C. number:'''
  
 
=== 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:'''  
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''Sigma factor:'''  
  
−
* '''Regulation:''' expressed in the absence of glutamine [http://www.ncbi.nlm.nih.gov/sites/entrez/8636055 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' repressed by [[GlnR]]-[[GlnA]] complex [http://www.ncbi.nlm.nih.gov/sites/entrez/8636055 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 116: Line 113:
 
* '''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]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 127: Line 122:
  
 
# 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]
 
# 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]
 
−
# 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]
 
−
# 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]
 
−
# 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]
 
−
# 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]
 
−
# 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 15:01, 31 March 2009

  • Description: transketolase

Gene name tkt
Synonyms tktA
Essential no
Product transketolase
Function pentose phosphate pathway
MW, pI 72 kDa, 4.803
Gene length, protein length 2001 bp, 667 aa
Immediate neighbours ynzC, yneE
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
Tkt 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: phosphorylated on ser/ thr/ tyr PubMed
  • 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

  • Operon:
  • Sigma factor:
  • Regulation:
  • Regulatory mechanism:
  • 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. Lévine 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 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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