Difference between revisions of "Sandbox"

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* '''Description:''' transcriptional repressor, regulation of fatty acid degradation <br/><br/>
+
* '''Description:''' fructose 1,6-bisphosphate aldolase, glycolytic/ gluconeogenic enzyme<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'''
−
|''fadR''
+
|''fbaA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ysiA''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''fba, fba1, tsr ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional repressor 
+
|style="background:#ABCDEF;" align="center"| '''Product''' || fructose-1,6-bisphosphate aldolase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of fatty acid degradation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 6.118 
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30,2 kDa, 5.03
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 582 bp, 194 aa
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 855 bp, 285 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fadB]]'', ''[[lcfA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spo0F]]'', ''[[ywjH]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14815&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|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)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ysiA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:fbaA_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/>
 +
  
 
=The gene=
 
=The gene=
Line 35: Line 36:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU28550
+
* '''Locus tag:''' BSU37120
  
 
===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/lcfA-ysiAB-etfBA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fbaA-ywjH.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12330]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10412]
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=The protein=
 
=The protein=
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''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
  
−
* '''Protein family:'''
+
* '''Protein family:''' class II fructose-bisphosphate aldolase family (according to Swiss-Prot) class II fructose-bisphosphate aldolase family
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[FbaB]]
  
 
=== 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:'''
+
* '''Modification:''' phosphorylation on Thr-212 AND Thr-234 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
−
* '''Cofactor(s):'''
+
* '''Cofactor(s):''' 2 x zinc ion
  
−
* '''Effectors of protein activity:'''
+
* '''Effectors of protein activity:''' inhibited by alpha-keto acids [http://www.ncbi.nlm.nih.gov/pubmed/24624 PubMed]
  
 
* '''Interactions:'''
 
* '''Interactions:'''
Line 78: Line 81:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P94548 P94548]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P13243 P13243]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28550]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37120]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.2.13 4.1.2.13] 3 4.1.2.13]
  
 
=== 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:'''  
+
* '''Regulation:''' constitutively expressed [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:'''  
  
−
* '''Expression vector:'''
+
* '''Expression vector:''' pGP395 (N-terminal His-tag, in [[pWH844]]), pGP88 (N-terminal Strep-tag, for [[SPINE]], expression in ''B. subtilis'', in [[pGP380]])
−
       
+
−
* '''lacZ fusion:'''
+
* '''lacZ fusion:''' pGP601 (in [[pAC6]])
  
 
* '''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:'''
Line 118: Line 125:
 
=References=
 
=References=
  
−
<pubmed>17189250, </pubmed>
+
<pubmed>17218307, </pubmed>
−
# Matsuoka H, Hirooka K, Fujita Y. (2007) Organization and function of the YsiA regulon of Bacillus subtilis involved in fatty acid degradation. ''J Biol Chem. '' '''Feb 23;282(8):''' 5180-94. [http://www.ncbi.nlm.nih.gov/sites/entrez/17189250 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]
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID 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]
 +
# 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: fructose 1,6-bisphosphate aldolase, glycolytic/ gluconeogenic enzyme

Gene name fbaA
Synonyms fba, fba1, tsr
Essential yes
Product fructose-1,6-bisphosphate aldolase
Function enzyme in glycolysis/ gluconeogenesis
MW, pI 30,2 kDa, 5.03
Gene length, protein length 855 bp, 285 amino acids
Immediate neighbours spo0F, ywjH
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
FbaA context.gif
This image was kindly provided by SubtiList




The gene

Basic information

  • Locus tag: BSU37120

Phenotypes of a mutant

essential PubMed

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

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
  • Protein family: class II fructose-bisphosphate aldolase family (according to Swiss-Prot) class II fructose-bisphosphate aldolase family
  • Paralogous protein(s): FbaB

Extended information on the protein

  • Kinetic information:
  • Domains:
    • 2 x Dihydroxyacetone phosphate binding domain (210–212), (231–234)
  • Modification: phosphorylation on Thr-212 AND Thr-234 PubMed
  • Cofactor(s): 2 x zinc ion
  • Effectors of protein activity: inhibited by alpha-keto acids PubMed
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Binds 2 zinc ions per subunit. One is catalytic and the other provides a structural contribution

Expression and regulation

  • Sigma factor:
  • Regulation: constitutively expressed PubMed
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector: pGP395 (N-terminal His-tag, in pWH844), pGP88 (N-terminal Strep-tag, for SPINE, expression in B. subtilis, in pGP380)
  • lacZ fusion: pGP601 (in pAC6)
  • 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

  1. 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. PubMed
  2. 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. PubMed
  3. Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
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