Difference between revisions of "Sandbox"
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| − | * '''Description:''' | + | * '''Description:''' DEAD-box RNA helicase<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''' | ||
| − | |'' | + | |''cshA'' |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' | + | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydbR'' |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''Essential''' || | + | |style="background:#ABCDEF;" align="center"| '''Essential''' || no |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''Product''' || | + | |style="background:#ABCDEF;" align="center"| '''Product''' || DEAD-box RNA helicase |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"|'''Function''' || | + | |style="background:#ABCDEF;" align="center"|'''Function''' || RNA helicase |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || | + | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 57 kDa, 9.89 |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || | + | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1533 bp, 511 aa |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ | + | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[murF]]'', ''[[ydbS]]'' |
|- | |- | ||
| − | |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:CAB12265]+-newId sequences] <br/> (Barbe ''et al.'', 2009)''' |
|- | |- | ||
| − | |colspan="2" | '''Genetic context''' <br/> [[Image: | + | |colspan="2" | '''Genetic context''' <br/> [[Image:ydbR_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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<br/><br/> | <br/><br/> | ||
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=The gene= | =The gene= | ||
| Line 43: | Line 38: | ||
===Phenotypes of a mutant === | ===Phenotypes of a mutant === | ||
| − | |||
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=== Database entries === | === Database entries === | ||
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* '''DBTBS entry:''' no entry | * '''DBTBS entry:''' no entry | ||
| − | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+ | + | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12085] |
=== Additional information=== | === Additional information=== | ||
| Line 59: | Line 52: | ||
=== Basic information/ Evolution === | === Basic information/ Evolution === | ||
| − | * '''Catalyzed reaction/ biological activity:''' | + | * '''Catalyzed reaction/ biological activity:''' RNA helicase |
| − | * '''Protein family:''' | + | * '''Protein family:''' DEAD-box RNA helicase |
| − | * '''Paralogous protein(s):''' | + | * '''Paralogous protein(s):''' [[CshB]], [[DeaD]], [[YfmL]] |
=== Extended information on the protein === | === Extended information on the protein === | ||
| Line 79: | Line 72: | ||
* '''Interactions:''' | * '''Interactions:''' | ||
| − | * '''Localization:''' Cytoplasm | + | * '''Localization:''' Cytoplasm cytoplasma, colocalizes with the ribosomes [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed] |
=== Database entries === | === Database entries === | ||
| Line 87: | Line 80: | ||
* '''Swiss prot entry:''' | * '''Swiss prot entry:''' | ||
| − | * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+ | + | * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU04580] |
* '''E.C. number:''' | * '''E.C. number:''' | ||
| Line 97: | Line 90: | ||
* '''Operon:''' | * '''Operon:''' | ||
| − | * ''' | + | * '''Sigma factor:''' |
* '''Regulation:''' | * '''Regulation:''' | ||
| Line 115: | Line 108: | ||
* '''GFP fusion:''' | * '''GFP fusion:''' | ||
| − | * '''two-hybrid system:''' | + | * '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab |
* '''Antibody:''' | * '''Antibody:''' | ||
=Labs working on this gene/protein= | =Labs working on this gene/protein= | ||
| + | |||
| + | [[Mohamed Marahiel]], Marburg University, Germany [http://www.uni-marburg.de/fb15/fachgebiete/bio/marahiel?language_sync=1 homepage] | ||
=Your additional remarks= | =Your additional remarks= | ||
| Line 125: | Line 120: | ||
=References= | =References= | ||
| + | # Hunger, K., Beckering, C. L., Wiegeshoff, F., Graumann, P. L. & Marahiel, M. A. (2006). Cold-induced putative DEAD box RNA helicases CshA and CshB are essential for cold adaptation and interact with cold shock protein B in ''Bacillus subtilis''. J Bacteriol. 188:240-248. [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed] | ||
| + | # Ando, Y. and K. Nakamura (2006) ''Bacillus subtilis'' DEAD protein YdbR possesses ATPase, RNA binding, and RNA unwinding activities.''Biosci. Biotechnol. Biochem.'' '''70:''' 1606-1615. [http://www.ncbi.nlm.nih.gov/sites/entrez/16861794 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 01:30, 30 April 2009
- Description: DEAD-box RNA helicase
| Gene name | cshA |
| Synonyms | ydbR |
| Essential | no |
| Product | DEAD-box RNA helicase |
| Function | RNA helicase |
| MW, pI | 57 kDa, 9.89 |
| Gene length, protein length | 1533 bp, 511 aa |
| Immediate neighbours | murF, ydbS |
| Get the DNA and protein sequences (Barbe et al., 2009) | |
Genetic context 
This image was kindly provided by SubtiList
| |
Contents
The gene
Basic information
- Coordinates:
Phenotypes of a mutant
Database entries
- DBTBS entry: no entry
- SubtiList entry: [1]
Additional information
The protein
Basic information/ Evolution
- Catalyzed reaction/ biological activity: RNA helicase
- Protein family: DEAD-box RNA helicase
Extended information on the protein
- Kinetic information:
- Domains:
- Modification:
- Cofactor(s):
- Effectors of protein activity:
- Interactions:
- Localization: Cytoplasm cytoplasma, colocalizes with the ribosomes PubMed
Database entries
- Structure:
- Swiss prot entry:
- KEGG entry: [2]
- E.C. number:
Additional information
Expression and regulation
- Operon:
- Sigma factor:
- Regulation:
- Regulatory mechanism:
- Additional information:
Biological materials
- Mutant:
- Expression vector:
- lacZ fusion:
- GFP fusion:
- two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab
- Antibody:
Labs working on this gene/protein
Mohamed Marahiel, Marburg University, Germany homepage
Your additional remarks
References
- Hunger, K., Beckering, C. L., Wiegeshoff, F., Graumann, P. L. & Marahiel, M. A. (2006). Cold-induced putative DEAD box RNA helicases CshA and CshB are essential for cold adaptation and interact with cold shock protein B in Bacillus subtilis. J Bacteriol. 188:240-248. PubMed
- Ando, Y. and K. Nakamura (2006) Bacillus subtilis DEAD protein YdbR possesses ATPase, RNA binding, and RNA unwinding activities.Biosci. Biotechnol. Biochem. 70: 1606-1615. PubMed
- Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
