Difference between revisions of "Sandbox"

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* '''Description:''' protein tyrosine kinase <br/><br/>
+
* '''Description:''' unknown <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'''
|''ptkA''
+
|''ynzC''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywqD ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || protein tyrosine kinase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || protein phosphorylation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 9.628  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 8 kDa, 10.285  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 711 bp, 237 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 231 bp, 77 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ptpZ]]'', ''[[tkmA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yneB]]'', ''[[tkt]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15642&#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:CAB13672&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:ywqD_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ynzC_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 29: Line 29:
 
__TOC__
 
__TOC__
  
<br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
Line 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
* '''Locus tag:''' BSU36250
+
* '''Locus tag:''' BSU17880
  
 
===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 ===
  
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ywqCD.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yneAB-ynzC.html]
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12508]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13466]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
* '''Catalyzed reaction/ biological activity:''' ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate (according to Swiss-Prot), autophosphorylation, phosphorylation of [[YwqF]], [[TuaD]], [[Ssb]], [[YwpH]]
+
* '''Catalyzed reaction/ biological activity:'''  
  
* '''Protein family:''' cpsD/capB family (according to Swiss-Prot), BY-kinase
+
* '''Protein family:''' UPF0291 family (according to Swiss-Prot)
  
* '''Paralogous protein(s):''' [[EpsB]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 64: Line 62:
 
* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
* '''Domains:''' single BY-kinase domain
+
* '''Domains:'''  
  
* '''Modification:''' autophosphorylation at residues Y225, Y227 and Y228 (primary site)
+
* '''Modification:'''
  
* '''Cofactor(s):''' ATP
+
* '''Cofactor(s):'''
  
* '''Effectors of protein activity:''' [[TkmA]] - transmembrane modulator, activates PtkA autophosphorylation and substrate phosphorylation [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]
+
* '''Effectors of protein activity:'''
  
* '''Interactions:''' [[PtkA]]-[[TkmA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]
+
* '''Interactions:'''
  
* '''Localization:'''
+
* '''Localization:''' cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
  
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2VED 2VED] (CapB, the homolog in ''Staphylococcus aureus'')
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2HEP 2HEP] (NMR), [http://www.rcsb.org/pdb/explore.do?structureId=3BHP 3BHP]
  
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P96716 P96716]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31818 O31818]
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU36250]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU17880]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 90: Line 88:
 
=Expression and regulation=
 
=Expression and regulation=
  
* '''Operon:''' ''[[tkmA]]-[[ptkA]]-[[ptpZ]]-[[ywqF]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]
+
* '''Operon:'''  
  
* '''[[Sigma factor]]:'''  
+
* '''[[[[Sigma factor]]]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 98: Line 96:
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
* '''Mutant:''' KO strain created with pMUTIN-2, available from [[Ivan Mijakovic]]
+
* '''Mutant:'''
  
* '''Expression vector:''' pQE-30, N-terminally 6xHis-tagged, available from [[Ivan Mijakovic]]
+
* '''Expression vector:'''
 
          
 
          
* '''lacZ fusion:''' in a KO strain created with pMUTIN-2, available from [[Ivan Mijakovic]]
+
* '''lacZ fusion:'''
  
* '''GFP fusion:''' CFP-fusion, available from [[Ivan Mijakovic]]
+
* '''GFP fusion:'''
  
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
Line 115: Line 113:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
[[Ivan Mijakovic]], Thiverval-Grignon, France
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 121: Line 118:
 
=References=
 
=References=
  
<pubmed>5,3,1,0,5,8,2,1, 12970183, 15741737, 15866923, 17367396, 19258708 </pubmed>
+
<pubmed>8,2,3,7,8,4,8,1, </pubmed>
 +
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 13:46, 8 June 2009

  • Description: unknown

Gene name ynzC
Synonyms
Essential no
Product unknown
Function unknown
MW, pI 8 kDa, 10.285
Gene length, protein length 231 bp, 77 aa
Immediate neighbours yneB, tkt
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YnzC context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU17880

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: UPF0291 family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cytoplasm (according to Swiss-Prot)

Database entries

  • KEGG entry: [3]
  • E.C. number:

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

U N Wiesmann, S DiDonato, N N Herschkowitz
Effect of chloroquine on cultured fibroblasts: release of lysosomal hydrolases and inhibition of their uptake.
Biochem Biophys Res Commun: 1975, 66(4);1338-43
[PubMed:4] [WorldCat.org] [DOI] (I p)

R J Smith, R G Bryant
Metal substitutions incarbonic anhydrase: a halide ion probe study.
Biochem Biophys Res Commun: 1975, 66(4);1281-6
[PubMed:3] [WorldCat.org] [DOI] (P p)

K S Bose, R H Sarma
Delineation of the intimate details of the backbone conformation of pyridine nucleotide coenzymes in aqueous solution.
Biochem Biophys Res Commun: 1975, 66(4);1173-9
[PubMed:2] [WorldCat.org] [DOI] (I p)

K Moroi, T Sato
Comparison between procaine and isocarboxazid metabolism in vitro by a liver microsomal amidase-esterase.
Biochem Pharmacol: 1975, 24(16);1517-21
[PubMed:8] [WorldCat.org] [DOI] (I p)

T R Anderson, T A Slotkin
Maturation of the adrenal medulla--IV. Effects of morphine.
Biochem Pharmacol: 1975, 24(16);1469-74
[PubMed:7] [WorldCat.org] [DOI] (I p)

A B Makar, K E McMartin, M Palese, T R Tephly
Formate assay in body fluids: application in methanol poisoning.
Biochem Med: 1975, 13(2);117-26
[PubMed:1] [WorldCat.org] [DOI] (P p)

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed