Difference between revisions of "Sandbox"
| Line 1: | Line 1: | ||
| − | * '''Description:''' regulation | + | * '''Description:''' two-component sensor kinase for exoenzyme and competence regulation <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''' | ||
| − | |'' | + | |''degS'' |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' | + | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''sacU '' |
|- | |- | ||
|style="background:#ABCDEF;" align="center"| '''Essential''' || no | |style="background:#ABCDEF;" align="center"| '''Essential''' || no | ||
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''Product''' || | + | |style="background:#ABCDEF;" align="center"| '''Product''' || two-component sensor kinase (NarL family) |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"|'''Function''' || | + | |style="background:#ABCDEF;" align="center"|'''Function''' || regulation of degradative enzyme and genetic competence |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || | + | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 44 kDa, 5.988 |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || | + | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1155 bp, 385 aa |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ | + | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[degU]]'', ''[[yvyE]]'' |
|- | |- | ||
| − | |colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS: | + | |colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15567]+-newId sequences] <br/> (Barbe ''et al.'', 2009)''' |
|- | |- | ||
| − | |colspan="2" | '''Genetic context''' <br/> [[Image: | + | |colspan="2" | '''Genetic context''' <br/> [[Image:degS_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 35: | Line 35: | ||
=== Basic information === | === Basic information === | ||
| − | * '''Locus tag:''' | + | * '''Locus tag:''' BSU35500 |
===Phenotypes of a mutant === | ===Phenotypes of a mutant === | ||
| Line 41: | Line 41: | ||
=== Database entries === | === Database entries === | ||
| − | * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ | + | * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/degSU.html] |
| − | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+ | + | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10392] |
=== Additional information=== | === Additional information=== | ||
| Line 52: | Line 52: | ||
=== Basic information/ Evolution === | === Basic information/ Evolution === | ||
| − | * '''Catalyzed reaction/ biological activity:''' | + | * '''Catalyzed reaction/ biological activity:''' ATP + protein L-histidine = ADP + protein N-phospho-L-histidine (according to Swiss-Prot) autophosphorylation, autodephosphorylation, phosphorylation of [[DegU]] on Asp-56 [http://www.ncbi.nlm.nih.gov/sites/entrez/1901568 PubMed] |
* '''Protein family:''' | * '''Protein family:''' | ||
| Line 64: | Line 64: | ||
* '''Domains:''' | * '''Domains:''' | ||
| − | * '''Modification:''' | + | ** aa 12 ... 170: unknown DegS domain |
| + | ** aa 180 ... 248: HisKA_3 domain (autophosphorylation) | ||
| + | ** aa 289 ... 384: HATPase_c | ||
| + | |||
| + | * '''Modification:''' phosphorylation on Ser-76 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], autophosphorylation on His-189 | ||
* '''Cofactor(s):''' | * '''Cofactor(s):''' | ||
| − | * '''Effectors of protein activity:''' | + | * '''Effectors of protein activity:''' [[DegQ]] |
| − | * '''Interactions:''' | + | * '''Interactions:''' [[DegS]]-[[DegU]], [[DegS]]-[[DegQ]] |
| − | * '''Localization:''' | + | * '''Localization:''' Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] |
=== Database entries === | === Database entries === | ||
| Line 78: | Line 82: | ||
* '''Structure:''' | * '''Structure:''' | ||
| − | * '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/ | + | * '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P13799 P13799] |
| − | * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+ | + | * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU35500] |
* '''E.C. number:''' | * '''E.C. number:''' | ||
| Line 88: | Line 92: | ||
=Expression and regulation= | =Expression and regulation= | ||
| − | * '''Operon:''' ''[[ | + | * '''Operon:''''' [[degS]]-[[degU]]'' |
| − | * '''[[Sigma factor]]:''' [[ | + | * '''[[Sigma factor]]:''' [[SigA]] |
| − | * '''Regulation:''' | + | * '''Regulation:''' induced in the presence of ammonium ([[TnrA]]) |
| − | * '''Regulatory mechanism:''' | + | * '''Regulatory mechanism:''' [[TnrA]]: repression, [[DegU]]: positive autoregulation |
* '''Additional information:''' | * '''Additional information:''' | ||
| Line 113: | Line 117: | ||
=Labs working on this gene/protein= | =Labs working on this gene/protein= | ||
| + | |||
| + | [[Tarek Msadek]], Institut Pasteur, Paris, France | ||
=Your additional remarks= | =Your additional remarks= | ||
| Line 118: | Line 124: | ||
=References= | =References= | ||
| − | <pubmed> | + | <pubmed>17850253,12471443,14563871,1459944,1901568,10094672,,16479537, 17218307 </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 09:02, 13 June 2009
- Description: two-component sensor kinase for exoenzyme and competence regulation
| Gene name | degS |
| Synonyms | sacU |
| Essential | no |
| Product | two-component sensor kinase (NarL family) |
| Function | regulation of degradative enzyme and genetic competence |
| MW, pI | 44 kDa, 5.988 |
| Gene length, protein length | 1155 bp, 385 aa |
| Immediate neighbours | degU, yvyE |
| Get the DNA and protein sequences (Barbe et al., 2009) | |
Genetic context 
This image was kindly provided by SubtiList
| |
Contents
The gene
Basic information
- Locus tag: BSU35500
Phenotypes of a mutant
Database entries
- DBTBS entry: [1]
- SubtiList entry: [2]
Additional information
The protein
Basic information/ Evolution
- Catalyzed reaction/ biological activity: ATP + protein L-histidine = ADP + protein N-phospho-L-histidine (according to Swiss-Prot) autophosphorylation, autodephosphorylation, phosphorylation of DegU on Asp-56 PubMed
- Protein family:
- Paralogous protein(s):
Extended information on the protein
- Kinetic information:
- Domains:
- aa 12 ... 170: unknown DegS domain
- aa 180 ... 248: HisKA_3 domain (autophosphorylation)
- aa 289 ... 384: HATPase_c
- Modification: phosphorylation on Ser-76 PubMed, autophosphorylation on His-189
- Cofactor(s):
- Effectors of protein activity: DegQ
- Localization: Cytoplasm (Homogeneous) PubMed
Database entries
- Structure:
- Swiss prot entry: P13799
- KEGG entry: [3]
- E.C. number:
Additional information
Expression and regulation
- Regulation: induced in the presence of ammonium (TnrA)
- Additional information:
Biological materials
- Mutant:
- Expression vector:
- lacZ fusion:
- GFP fusion:
- two-hybrid system:
- Antibody:
Labs working on this gene/protein
Tarek Msadek, Institut Pasteur, Paris, France
Your additional remarks
References
Kazuo Kobayashi
Gradual activation of the response regulator DegU controls serial expression of genes for flagellum formation and biofilm formation in Bacillus subtilis.
Mol Microbiol: 2007, 66(2);395-409
[PubMed:17850253]
[WorldCat.org]
[DOI]
(P p)
Boris Macek, Ivan Mijakovic, Jesper V Olsen, Florian Gnad, Chanchal Kumar, Peter R Jensen, Matthias Mann
The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis.
Mol Cell Proteomics: 2007, 6(4);697-707
[PubMed:17218307]
[WorldCat.org]
[DOI]
(P p)
Jean-Christophe Meile, Ling Juan Wu, S Dusko Ehrlich, Jeff Errington, Philippe Noirot
Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory.
Proteomics: 2006, 6(7);2135-46
[PubMed:16479537]
[WorldCat.org]
[DOI]
(P p)
Leif Steil, Tamara Hoffmann, Ina Budde, Uwe Völker, Erhard Bremer
Genome-wide transcriptional profiling analysis of adaptation of Bacillus subtilis to high salinity.
J Bacteriol: 2003, 185(21);6358-70
[PubMed:14563871]
[WorldCat.org]
[DOI]
(P p)
U Mäder, H Antelmann, T Buder, M K Dahl, M Hecker, G Homuth
Bacillus subtilis functional genomics: genome-wide analysis of the DegS-DegU regulon by transcriptomics and proteomics.
Mol Genet Genomics: 2002, 268(4);455-67
[PubMed:12471443]
[WorldCat.org]
[DOI]
(P p)
C Fabret, V A Feher, J A Hoch
Two-component signal transduction in Bacillus subtilis: how one organism sees its world.
J Bacteriol: 1999, 181(7);1975-83
[PubMed:10094672]
[WorldCat.org]
[DOI]
(P p)
K Mukai, M Kawata-Mukai, T Tanaka
Stabilization of phosphorylated Bacillus subtilis DegU by DegR.
J Bacteriol: 1992, 174(24);7954-62
[PubMed:1459944]
[WorldCat.org]
[DOI]
(P p)
M K Dahl, T Msadek, F Kunst, G Rapoport
Mutational analysis of the Bacillus subtilis DegU regulator and its phosphorylation by the DegS protein kinase.
J Bacteriol: 1991, 173(8);2539-47
[PubMed:1901568]
[WorldCat.org]
[DOI]
(P p)
- Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
