Difference between revisions of "Sandbox"

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* '''Description:''' RNase Mini-III <br/><br/>
+
* '''Description:''' Fur-regulated basic protein, acts as RNA chaperone for fsrA <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'''
−
|''mrnC''
+
|''fbpA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yazC''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydbN''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || RNase Mini-III
+
|style="background:#ABCDEF;" align="center"| '''Product''' || Fur-regulated basic protein, <br/>acts as RNA chaperone for fsrA
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || maturation of 23S rRNA
+
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA chaperone
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 9.153 
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || xx,x kDa, 9.50
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 429 bp, 143 aa
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 159 bp, 53 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cysS]]'', ''[[yacO]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fbpB]]'', ''[[ydbO]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11871&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_nucleotide.txt    Gene sequence      (+200bp)  ]'''
 +
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yazC_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:FbpA_fbpB_context.jpeg]]
−
<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=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00950
+
* '''Locus tag:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gltX-cysES-yazC-yacOP.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12702]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12081]
  
 
=== Additional information===
 
=== Additional information===
  
 +
The sequence of the former ydbN gene was corrected, and does now contain two genes, [[fbpA]] and [[fbpB]]. [http://www.ncbi.nlm.nih.gov/sites/entrez/18697947 PubMed]
  
 
=The protein=
 
=The protein=
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* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' RNase III family (but lacks the dsRNA-binding domain)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:''' [[RplC]] binding to the precursor 23S rRNA stimulates MrnC activity [http://www.ncbi.nlm.nih.gov/sites/entrez/19154332 PubMed]
+
* '''Effectors of protein activity:'''
  
 
* '''Interactions:'''
 
* '''Interactions:'''
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00950]
+
* '''KEGG entry:''' no entry
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[gltX]]-[[cysE]]-[[cysS]]-[[mrnC]]-[[yacO]]-[[yacP]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/7510287 PubMed]
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/7510287 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' repression by cysteine ([[T-box]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/7510287 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' [[T-box]], overlaps a transcription terminator upstream of ''[[cysE]]'': transcription antitermination [http://www.ncbi.nlm.nih.gov/sites/entrez/7510287 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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* '''Expression vector:'''
 
* '''Expression vector:'''
−
       
+
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Ciaran Condon]], IBPC, Paris, France [http://www.ibpc.fr/UPR9073/condon/index_en.html Homepage]
 
−
 
−
[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>19154332, </pubmed>
+
<pubmed>18697947, </pubmed>
−
# Redko, Y. & Condon, C. (2009) Ribosomal protein L3 bound to 23S precursor rRNA stimulates its maturation by Mini-III ribonuclease.  ''Mol. Microbiol.'' '''71:''' 1145-1154. [http://www.ncbi.nlm.nih.gov/sites/entrez/19154332 PubMed]
+
# Gaballa A, Antelmann H, Aguilar C, Khakh SK, Song KB, Smaldone GT, Helmann JD. (2008) The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins.  ''Proc Natl Acad Sci U S A.'' '''Aug 19;105(33):''' 11927-32. [http://www.ncbi.nlm.nih.gov/sites/entrez/18697947 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 22:44, 12 June 2009

  • Description: Fur-regulated basic protein, acts as RNA chaperone for fsrA

Gene name fbpA
Synonyms ydbN
Essential no
Product Fur-regulated basic protein,
acts as RNA chaperone for fsrA
Function RNA chaperone
MW, pI xx,x kDa, 9.50
Gene length, protein length 159 bp, 53 amino acids
Immediate neighbours fbpB, ydbO
Gene sequence (+200bp) Protein sequence
Genetic context
FbpA fbpB context.jpeg




The gene

Basic information

  • Locus tag:

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The sequence of the former ydbN gene was corrected, and does now contain two genes, fbpA and fbpB. PubMed

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: no entry
  • 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

Ahmed Gaballa, Haike Antelmann, Claudio Aguilar, Sukhjit K Khakh, Kyung-Bok Song, Gregory T Smaldone, John D Helmann
The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins.
Proc Natl Acad Sci U S A: 2008, 105(33);11927-32
[PubMed:18697947] [WorldCat.org] [DOI] (I p)

  1. Gaballa A, Antelmann H, Aguilar C, Khakh SK, Song KB, Smaldone GT, Helmann JD. (2008) The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins. Proc Natl Acad Sci U S A. Aug 19;105(33): 11927-32. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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