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''' | ||
| − | |'' | + | |''deaD'' |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' '' | + | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxiN '' |
|- | |- | ||
|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''' || ATP-dependent 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''' || 53 kDa, 7.706 |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || | + | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1437 bp, 479 aa |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ | + | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxiO]]'', ''[[yxiM]]'' |
|- | |- | ||
| − | |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:CAB15947]+-newId sequences] <br/> (Barbe ''et al.'', 2009)''' |
|- | |- | ||
|- | |- | ||
|- | |- | ||
| − | |colspan="2" | '''Genetic context''' <br/> [[Image: | + | |colspan="2" | '''Genetic context''' <br/> [[Image:deaD_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 31: | Line 31: | ||
__TOC__ | __TOC__ | ||
| − | + | <br/><br/> | |
=The gene= | =The gene= | ||
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* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yxiM-deaD.html] | * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yxiM-deaD.html] | ||
| − | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+ | + | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11143] |
=== Additional information=== | === Additional information=== | ||
| Line 54: | Line 54: | ||
=== 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):''' [[CshA]], [[CshB]], [[YfmL]] |
=== Extended information on the protein === | === Extended information on the protein === | ||
| Line 65: | Line 65: | ||
* '''Domains:''' | * '''Domains:''' | ||
| + | **Helicase domain 1: AS 1-203 | ||
| + | **Linker region: AS 204-212 | ||
| + | **Helicase domain 2: AS 207-368 | ||
| + | **RNA-binding domain: AS 404-479 | ||
* '''Modification:''' | * '''Modification:''' | ||
| Line 82: | Line 86: | ||
* '''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+BSU39110] |
* '''E.C. number:''' | * '''E.C. number:''' | ||
| Line 92: | Line 96: | ||
* '''Operon:''' | * '''Operon:''' | ||
| − | * ''' | + | * '''Sigma factor:''' |
* '''Regulation:''' | * '''Regulation:''' | ||
| Line 102: | Line 106: | ||
=Biological materials = | =Biological materials = | ||
| − | * '''Mutant:''' | + | * '''Mutant:''' GP1121 (tet), available in the [[Stülke]] lab |
* '''Expression vector:''' | * '''Expression vector:''' | ||
| Line 110: | Line 114: | ||
* '''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= | ||
| + | |||
| + | [[Dagmar Klostermeier]], Biozentrum Basel, Switzerland [http://www.biozentrum.unibas.ch/klostermeier/index.html homepage] | ||
=Your additional remarks= | =Your additional remarks= | ||
| Line 120: | Line 126: | ||
=References= | =References= | ||
| + | # Caruthers, J. M., Hu, Y. & McKay, D. B. (2006). Structure of the second domain of the ''Bacillus subtilis'' DEAD-box RNA helicase YxiN. Acta Crystallogr Sect F Struct Biol Cryst Commun 62, 1191-1195.[http://www.ncbi.nlm.nih.gov/pubmed/17142894 PubMed] | ||
| + | # Karginov, F. V., Caruthers, J. M., Hu, Y., McKay, D. B. & Uhlenbeck, O. C. (2005). YxiN is a modular protein combining a DEx(D/H) core and a specific RNA-binding domain. J Biol Chem 280, 35499-35505.[http://www.ncbi.nlm.nih.gov/pubmed/16118224 PubMed] | ||
| + | # Karow, A. R., Theissen, B. & Klostermeier, D. (2007). Authentic interdomain communication in an RNA helicase reconstituted by expressed protein ligation of two helicase domains. FEBS J 274, 463-473.[http://www.ncbi.nlm.nih.gov/pubmed/17229151 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 23:51, 16 April 2009
- Description: DEAD-box RNA helicase
| Gene name | deaD |
| Synonyms | yxiN |
| Essential | no |
| Product | ATP-dependent RNA helicase |
| Function | RNA helicase |
| MW, pI | 53 kDa, 7.706 |
| Gene length, protein length | 1437 bp, 479 aa |
| Immediate neighbours | yxiO, yxiM |
| 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: [1]
- SubtiList entry: [2]
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:
- Helicase domain 1: AS 1-203
- Linker region: AS 204-212
- Helicase domain 2: AS 207-368
- RNA-binding domain: AS 404-479
- Modification:
- Cofactor(s):
- Effectors of protein activity:
- Interactions:
- Localization:
Database entries
- Structure:
- Swiss prot entry:
- KEGG entry: [3]
- E.C. number:
Additional information
Expression and regulation
- Operon:
- Sigma factor:
- Regulation:
- Regulatory mechanism:
- Additional information:
Biological materials
- Mutant: GP1121 (tet), available in the Stülke lab
- 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
Dagmar Klostermeier, Biozentrum Basel, Switzerland homepage
Your additional remarks
References
- Caruthers, J. M., Hu, Y. & McKay, D. B. (2006). Structure of the second domain of the Bacillus subtilis DEAD-box RNA helicase YxiN. Acta Crystallogr Sect F Struct Biol Cryst Commun 62, 1191-1195.PubMed
- Karginov, F. V., Caruthers, J. M., Hu, Y., McKay, D. B. & Uhlenbeck, O. C. (2005). YxiN is a modular protein combining a DEx(D/H) core and a specific RNA-binding domain. J Biol Chem 280, 35499-35505.PubMed
- Karow, A. R., Theissen, B. & Klostermeier, D. (2007). Authentic interdomain communication in an RNA helicase reconstituted by expressed protein ligation of two helicase domains. FEBS J 274, 463-473.PubMed
- Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
