SubtiWiki - User contributions [en]

DeaD

2009-02-25T21:57:47Z

Stholen: /* Biological materials */

* '''Description:''' DEAD-box RNA helicase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''deaD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxiN ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || ATP-dependent RNA helicase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA helicase
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 53 kDa, 7.706
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1437 bp, 479 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxiO]]'', ''[[yxiM]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/deaD_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/deaD_protein.txt Protein sequence]'''
|-
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
|-
|colspan="2" | '''Genetic context''' [[Image:deaD_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:'''

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/deaD.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11143]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' RNA helicase

* '''Protein family:''' DEAD-box RNA helicase

* '''Paralogous protein(s):''' [[CshA]], [[CshB]], [[YfmL]]

=== 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:'''

* '''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=

=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.[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]

DeaD

2009-02-25T21:54:34Z

Stholen: /* Biological materials */

* '''Description:''' DEAD-box RNA helicase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''deaD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxiN ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || ATP-dependent RNA helicase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA helicase
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 53 kDa, 7.706
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1437 bp, 479 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxiO]]'', ''[[yxiM]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/deaD_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/deaD_protein.txt Protein sequence]'''
|-
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
|-
|colspan="2" | '''Genetic context''' [[Image:deaD_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:'''

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/deaD.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11143]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' RNA helicase

* '''Protein family:''' DEAD-box RNA helicase

* '''Paralogous protein(s):''' [[CshA]], [[CshB]], [[YfmL]]

=== 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:'''

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP1121 (spc), 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=

=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.[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]