Difference between revisions of "Sandbox"

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* '''Description:''' protein tyrosine kinase <br/><br/>
+
* '''Description:''' two-component response regulator, control of cellular responses to protein secretion stress <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''
+
|''cssR''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywqD ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvqA ''
 
|-
 
|-
 
|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''' || two-component response regulator
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || protein phosphorylation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || control of cellular responses to protein secretion stress
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 9.628  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 5.071  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 711 bp, 237 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 675 bp, 225 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ptpZ]]'', ''[[tkmA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[htrB]]'', ''[[cssS]]''
 
|-
 
|-
−
|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:CAB15291&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ywqD_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:cssR_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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__TOC__
 
__TOC__
  
−
<br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
Line 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU36250
+
* '''Locus tag:''' BSU33010
  
 
===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/cssRS.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12508]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14131]
  
 
=== 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:''' OmpR family of two-component response regulators
  
−
* '''Paralogous protein(s):''' [[EpsB]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''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:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P96716 P96716]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32192 O32192]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU36250]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33010]
  
 
* '''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]]:'''  
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* '''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>2,9,5,6,3,1,9,1, </pubmed>
 +
# Darmon E, Noone D, Masson A, Bron S, Kuipers OP, Devine KM, van Dijl JM. (2002) A novel class of heat and secretion stress-responsive genes is controlled by the autoregulated CssRS two-component system of Bacillus subtilis. ''J Bacteriol. '' '''184(20):''' 5661-71. [http://www.ncbi.nlm.nih.gov/sites/entrez/12270824 PubMed]
 +
# Hyyryläinen HL, Bolhuis A, Darmon E, Muukkonen L, Koski P, Vitikainen M, Sarvas M, Prágai Z, Bron S, van Dijl JM, Kontinen VP. (2001) A novel two-component regulatory system in Bacillus subtilis for the survival of severe secretion stress. ''Mol Microbiol. '' '''41(5):''' 1159-72. [http://www.ncbi.nlm.nih.gov/sites/entrez/11555295 PubMed]

Revision as of 12:46, 8 June 2009

  • Description: two-component response regulator, control of cellular responses to protein secretion stress

Gene name cssR
Synonyms yvqA
Essential no
Product two-component response regulator
Function control of cellular responses to protein secretion stress
MW, pI 26 kDa, 5.071
Gene length, protein length 675 bp, 225 aa
Immediate neighbours htrB, cssS
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
CssR context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU33010

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: OmpR family of two-component response regulators
  • 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

  • Structure:
  • 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

Y W Chow, R Pietranico, A Mukerji
Studies of oxygen binding energy to hemoglobin molecule.
Biochem Biophys Res Commun: 1975, 66(4);1424-31
[PubMed:6] [WorldCat.org] [DOI] (P p)

W A Hendrickson, K B Ward
Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin.
Biochem Biophys Res Commun: 1975, 66(4);1349-56
[PubMed:5] [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)

J Marniemi, M G Parkki
Radiochemical assay of glutathione S-epoxide transferase and its enhancement by phenobarbital in rat liver in vivo.
Biochem Pharmacol: 1975, 24(17);1569-72
[PubMed:9] [WorldCat.org] [DOI] (P 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. Darmon E, Noone D, Masson A, Bron S, Kuipers OP, Devine KM, van Dijl JM. (2002) A novel class of heat and secretion stress-responsive genes is controlled by the autoregulated CssRS two-component system of Bacillus subtilis. J Bacteriol. 184(20): 5661-71. PubMed
  2. Hyyryläinen HL, Bolhuis A, Darmon E, Muukkonen L, Koski P, Vitikainen M, Sarvas M, Prágai Z, Bron S, van Dijl JM, Kontinen VP. (2001) A novel two-component regulatory system in Bacillus subtilis for the survival of severe secretion stress. Mol Microbiol. 41(5): 1159-72. PubMed
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