Difference between revisions of "Sandbox"

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* '''Description:''' fructose 1,6-bisphosphate aldolase, glycolytic/ gluconeogenic enzyme<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'''
−
|''fbaA''
+
|''fbpA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''fba, fba1, tsr ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydbN''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || fructose-1,6-bisphosphate aldolase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || Fur-regulated basic protein, <br/>acts as RNA chaperone for fsrA
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA chaperone
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30,2 kDa, 5.03
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || xx,x kDa, 9.50
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 855 bp, 285 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 159 bp, 53 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spo0F]]'', ''[[ywjH]]''
+
|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:CAB15729&#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:fbaA_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=
Line 36: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU37120
+
* '''Locus tag:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
essential  [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fbaA-ywjH.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10412]
+
* '''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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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate (according to Swiss-Prot) D-fructose 1,6-bisphosphate = dihydroxyacetone phosphate + D-glyceraldehyde 3-phosphate
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' class II fructose-bisphosphate aldolase family (according to Swiss-Prot) class II fructose-bisphosphate aldolase family
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[FbaB]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Domains:'''  
 
* '''Domains:'''  
−
** 2 x Dihydroxyacetone phosphate binding domain (210–212), (231–234)
 
  
−
* '''Modification:''' phosphorylation on Thr-212 AND Thr-234 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
+
* '''Modification:'''
  
−
* '''Cofactor(s):''' 2 x zinc ion
+
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:''' inhibited by alpha-keto acids [http://www.ncbi.nlm.nih.gov/pubmed/24624 PubMed]
+
* '''Effectors of protein activity:'''
  
 
* '''Interactions:'''
 
* '''Interactions:'''
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P13243 P13243]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37120]
+
* '''KEGG entry:''' no entry
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.2.13 4.1.2.13] 3 4.1.2.13]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
−
Binds 2 zinc ions per subunit. One is catalytic and the other provides a structural contribution
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
 
* '''Operon:'''  
 
* '''Operon:'''  
−
**''fbaA'' [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]
 
−
**''fbaA-[[ywjH]]'' [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]
 
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' constitutively expressed [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]
+
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''  
+
* '''Mutant:'''
  
−
* '''Expression vector:''' pGP395 (N-terminal His-tag, in [[pWH844]]), pGP88 (N-terminal Strep-tag, for [[SPINE]], expression in ''B. subtilis'', in [[pGP380]])
+
* '''Expression vector:'''
 
 
−
* '''lacZ fusion:''' pGP601 (in [[pAC6]])
+
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+
* '''two-hybrid system:'''  
  
 
* '''Antibody:'''
 
* '''Antibody:'''
Line 125: Line 119:
 
=References=
 
=References=
  
−
<pubmed>17218307, </pubmed>
+
<pubmed>18697947, </pubmed>
−
# Trach K, Chapman JW & Piggot P (1988) Complete sequence and transcriptional analysis of the ''spo0F'' region of the ''Bacillus subtilis'' chromosome ''J Bacteriol.'' '''170:''' 4194-4208. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+2457578 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]
−
# Ludwig H, Homuth G & Schmalisch M (2001) Transcription of glycolytic genes and operons in ''Bacillus subtilis'': evidence for the presence of multiple levels of control of the ''gapA'' operon  ''Mol Microbiol.''  '''41:''' 409-422. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707  [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
 

Revision as of 13:16, 8 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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