Difference between revisions of "Sandbox"

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−
* '''Description:''' tRNA-Thr
+
* '''Description:''' UDP glucose 6-dehydrogenase <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'''
−
|''trnB-Thr''
+
|''tuaD''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''trnE ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvhD ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transfer RNA-Thr
+
|style="background:#ABCDEF;" align="center"| '''Product''' || UDP glucose 6-dehydrogenase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of teichuronic acid
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length''' || 76 bp
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 6.107 
−
|-|-
 
−
 
 
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[trnB-Lys]]'', ''[[trnB-Val]]''
 
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/trnB-Thr_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1383 bp, 461 aa
−
|style="background:#FAF8CC;" align="center"|'''  '''
 
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:trnB-Thr_context.gif]]
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[tuaE]]'', ''[[tuaC]]''
 +
|-
 +
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15575&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:tuaD_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 31: Line 31:
 
<br/><br/>
 
<br/><br/>
  
−
<br/><br/><br/><br/><br/>
 
 
=The gene=
 
=The gene=
  
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:'''
+
* '''Locus tag:''' BSU35580
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 42: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/tuaABCDEFGH.html]
 +
 
 +
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12691]
 +
 
 +
=== Additional information===
 +
 
 +
 
 +
=The protein=
 +
 
 +
=== Basic information/ Evolution ===
 +
 
 +
* '''Catalyzed reaction/ biological activity:''' UDP-glucose + 2 NAD<sup>+</sup> + H<sub>2</sub>O = UDP-glucuronate + 2 NADH (according to Swiss-Prot)
 +
 
 +
* '''Protein family:''' UDP-glucose/GDP-mannose dehydrogenase family (according to Swiss-Prot)
 +
 
 +
* '''Paralogous protein(s):''' [[YtcA]], [[YwqF]]
 +
 
 +
=== Extended information on the protein ===
 +
 
 +
* '''Kinetic information:'''
 +
 
 +
* '''Domains:'''
 +
 
 +
* '''Modification:''' phosphorylation on a Tyr residue by [[PtkA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]
 +
 
 +
* '''Cofactor(s):'''
 +
 
 +
* '''Effectors of protein activity:''' [[PtkA]]-dependent phosphorylation stimulates TuaD activity [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]
 +
 
 +
* '''Interactions:'''
 +
 
 +
* '''Localization:''' cytoplasm (according to Swiss-Prot)
 +
 
 +
=== Database entries ===
 +
 
 +
* '''Structure:'''
 +
 
 +
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32271 O32271]
 +
 
 +
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU35580]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG00075]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.22 1.1.1.22]
−
 
−
* '''Structure:'''
 
  
 
=== Additional information===
 
=== Additional information===
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* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
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* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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* '''Antibody:'''
 
* '''Antibody:'''
  
−
=Labs working on this gene/RNA=
+
=Labs working on this gene/protein=
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 82: Line 118:
 
=References=
 
=References=
  
−
<pubmed>2414156, </pubmed>
+
<pubmed>12970183, </pubmed>
−
# Green CJ, Stewart GC, Hollis MA, Vold BS, Bott KF (1985) Nucleotide sequence of the ''Bacillus subtilis'' ribosomal RNA operon, ''rrnB''.''Nucl. Acids Res.'' '''37:''' 261-266. [http://www.ncbi.nlm.nih.gov/sites/entrez/2414156 PubMed]
+
# Mijakovic I, Poncet S, Boël G, Mazé A, Gillet S, Decottignies P, Grangeasse C, Jamet E, Doublet P, Le Maréchal P, Deutscher J (2003) Transmembrane modulator-dependent bacterial tyrosine kinase activates UDP-glucose dehydrogenases. EMBO J  22:4709-4718. [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 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 13:40, 8 June 2009

  • Description: UDP glucose 6-dehydrogenase

Gene name tuaD
Synonyms yvhD
Essential no
Product UDP glucose 6-dehydrogenase
Function biosynthesis of teichuronic acid
MW, pI 49 kDa, 6.107
Gene length, protein length 1383 bp, 461 aa
Immediate neighbours tuaE, tuaC
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
TuaD context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU35580

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: UDP-glucose + 2 NAD+ + H2O = UDP-glucuronate + 2 NADH (according to Swiss-Prot)
  • Protein family: UDP-glucose/GDP-mannose dehydrogenase family (according to Swiss-Prot)

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylation on a Tyr residue by PtkA PubMed
  • Cofactor(s):
  • Effectors of protein activity: PtkA-dependent phosphorylation stimulates TuaD activity PubMed
  • Interactions:
  • Localization: cytoplasm (according to Swiss-Prot)

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Operon:
  • 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

Ivan Mijakovic, Sandrine Poncet, Grégory Boël, Alain Mazé, Sylvie Gillet, Emmanuel Jamet, Paulette Decottignies, Christophe Grangeasse, Patricia Doublet, Pierre Le Maréchal, Josef Deutscher
Transmembrane modulator-dependent bacterial tyrosine kinase activates UDP-glucose dehydrogenases.
EMBO J: 2003, 22(18);4709-18
[PubMed:12970183] [WorldCat.org] [DOI] (P p)

  1. Mijakovic I, Poncet S, Boël G, Mazé A, Gillet S, Decottignies P, Grangeasse C, Jamet E, Doublet P, Le Maréchal P, Deutscher J (2003) Transmembrane modulator-dependent bacterial tyrosine kinase activates UDP-glucose dehydrogenases. EMBO J 22:4709-4718. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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