Difference between revisions of "Sandbox"

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−
* '''Description:''' transmembrane modulator of PtkA activity, activates PtkA autophosphorylation and substrate phosphorylation <br/><br/>
+
* '''Description:''' protein tyrosine kinase <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'''
−
|''tkmA''
+
|''ptkA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywqC ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywqD ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || modulator of PtkA activity
+
|style="background:#ABCDEF;" align="center"| '''Product''' || protein tyrosine kinase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || control of protein tyrosine phosphorylation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || protein phosphorylation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 4.61  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 9.628  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 744 bp, 248 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 711 bp, 237 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ptkA]]'', ''[[ywqB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ptpZ]]'', ''[[tkmA]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ywqC_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ywqD_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 38: Line 38:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
Accumulation of extra chromosome equivalents [http://www.ncbi.nlm.nih.gov/sites/entrez/17367396 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 43: Line 45:
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ywqCD.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ywqCD.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12507]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12508]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' autophosphorylation, phosphorylation of [[YwqF]], [[TuaD]], [[Ssb]], [[YwpH]]
  
−
* '''Protein family:'''
+
* '''Protein family:''' BY-kinase
  
−
* '''Paralogous protein(s):''' [[EpsA]]
+
* '''Paralogous protein(s):''' [[EpsB]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 62: Line 64:
 
* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:'''  
+
* '''Domains:''' single BY-kinase domain
  
−
* '''Modification:'''
+
* '''Modification:''' autophosphorylation at residues Y225, Y227 and Y228 (primary site)
  
−
* '''Cofactor(s):'''
+
* '''Cofactor(s):''' ATP
  
−
* '''Effectors of protein activity:'''
+
* '''Effectors of protein activity:''' [[TkmA]] - transmembrane modulator, activates PtkA autophosphorylation and substrate phosphorylation [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]
  
 
* '''Interactions:''' [[PtkA]]-[[TkmA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]
 
* '''Interactions:''' [[PtkA]]-[[TkmA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]
Line 76: Line 78:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2VED 2VED] (CapB, the homolog in ''Staphylococcus aureus'')
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU36260]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU36250]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 100: Line 102:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' KO strain created with pMUTIN-2, available from [[Ivan Mijakovic]]
  
−
* '''Expression vector:'''
+
* '''Expression vector:''' pQE-30, N-terminally 6xHis-tagged, available from [[Ivan Mijakovic]]
 
          
 
          
−
* '''lacZ fusion:'''
+
* '''lacZ fusion:''' in a KO strain created with pMUTIN-2, available from [[Ivan Mijakovic]]
  
−
* '''GFP fusion:'''
+
* '''GFP fusion:''' CFP-fusion, available from [[Ivan Mijakovic]]
  
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
Line 113: Line 115:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
[[Ivan Mijakovic]], Thiverval-Grignon, France
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 119: Line 122:
  
 
# 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]
 
# 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]
+
# Mijakovic I, Petranovic D, Deutscher J (2004) How tyrosine phosphorylation affects the UDP-glucose dehydrogenase activity of Bacillus subtilis YwqF. J Mol Microbiol Biotechnol 8:19-25.  [http://www.ncbi.nlm.nih.gov/sites/entrez/15741737 PubMed]
 +
# Mijakovic I, Musumeci L, Tautz L, Petranovic D, Edwards RA, Jensen PR, Mustelin T, Deutscher J, Bottini N (2005) In vitro characterization of the Bacillus subtilis protein tyrosine phosphatase YwqE. J Bacteriol 187(10):3384-3390 [http://www.ncbi.nlm.nih.gov/sites/entrez/15866923 PubMed]
 +
# Mijakovic I, Petranovic D, Macek B, Cepo T, Mann M, Davies J, Jensen PR, Vujaklija D (2006) Bacterial single-stranded DNA-binding proteins are phosphorylated on tyrosine. Nucl Acids Res 34:1588-1596.  [http://www.ncbi.nlm.nih.gov/sites/entrez/16549871 PubMed]
 +
# Petranovic D, Michelsen O, Zahradka K, Silva C, Petranovic M, Jensen PR, Mijakovic I (2007) Bacillus subtilis strain deficient for the protein-tyrosine kinase PtkA exhibits impaired DNA replication. Mol Microbiol 63:1797-1805. [http://www.ncbi.nlm.nih.gov/sites/entrez/17367396 PubMed]

Revision as of 17:25, 15 April 2009

  • Description: protein tyrosine kinase

Gene name ptkA
Synonyms ywqD
Essential no
Product protein tyrosine kinase
Function protein phosphorylation
MW, pI 25 kDa, 9.628
Gene length, protein length 711 bp, 237 aa
Immediate neighbours ptpZ, tkmA
Hier soll was neues rein
Genetic context
YwqD context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Accumulation of extra chromosome equivalents PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: autophosphorylation, phosphorylation of YwqF, TuaD, Ssb, YwpH
  • Protein family: BY-kinase
  • Paralogous protein(s): EpsB

Extended information on the protein

  • Kinetic information:
  • Domains: single BY-kinase domain
  • Modification: autophosphorylation at residues Y225, Y227 and Y228 (primary site)
  • Cofactor(s): ATP
  • Effectors of protein activity: TkmA - transmembrane modulator, activates PtkA autophosphorylation and substrate phosphorylation PubMed
  • Localization:

Database entries

  • Structure: 2VED (CapB, the homolog in Staphylococcus aureus)
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant: KO strain created with pMUTIN-2, available from Ivan Mijakovic
  • Expression vector: pQE-30, N-terminally 6xHis-tagged, available from Ivan Mijakovic
  • lacZ fusion: in a KO strain created with pMUTIN-2, available from Ivan Mijakovic
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Ivan Mijakovic, Thiverval-Grignon, France

Your additional remarks

References

  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. Mijakovic I, Petranovic D, Deutscher J (2004) How tyrosine phosphorylation affects the UDP-glucose dehydrogenase activity of Bacillus subtilis YwqF. J Mol Microbiol Biotechnol 8:19-25. PubMed
  3. Mijakovic I, Musumeci L, Tautz L, Petranovic D, Edwards RA, Jensen PR, Mustelin T, Deutscher J, Bottini N (2005) In vitro characterization of the Bacillus subtilis protein tyrosine phosphatase YwqE. J Bacteriol 187(10):3384-3390 PubMed
  4. Mijakovic I, Petranovic D, Macek B, Cepo T, Mann M, Davies J, Jensen PR, Vujaklija D (2006) Bacterial single-stranded DNA-binding proteins are phosphorylated on tyrosine. Nucl Acids Res 34:1588-1596. PubMed
  5. Petranovic D, Michelsen O, Zahradka K, Silva C, Petranovic M, Jensen PR, Mijakovic I (2007) Bacillus subtilis strain deficient for the protein-tyrosine kinase PtkA exhibits impaired DNA replication. Mol Microbiol 63:1797-1805. PubMed
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