Difference between revisions of "Sandbox"

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Line 1: Line 1:
−
* '''Description:''' enolase, glycolytic/ gluconeogenic enzyme<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'''
−
|''eno''
+
|''fbaA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''fba, fba1, tsr ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || enolase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || fructose-1,6-bisphosphate aldolase
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
 
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46,4 kDa, 4.49
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30,2 kDa, 5.03
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1290 bp, 430 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 855 bp, 285 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pgm]]'', ''[[yvgK]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spo0F]]'', ''[[ywjH]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/eno_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/fbaA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/eno_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/fbaA_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:eno_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:fbaA_context.gif]]
 
|-
 
|-
 
|}
 
|}
Line 36: Line 36:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 3475589 - 3476878
+
* '''Coordinates:''' 3807538 - 3808392
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 44: Line 44:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fbaA-ywjH.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10899]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10412]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' 2-phospho-D-glycerate = phosphoenolpyruvate + H(2)O
+
* '''Catalyzed reaction/ biological activity:''' D-fructose 1,6-bisphosphate = dihydroxyacetone phosphate + D-glyceraldehyde 3-phosphate
  
−
* '''Protein family:''' enolase family
+
* '''Protein family:''' class II fructose-bisphosphate aldolase family.
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[FbaB]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 65: Line 65:
  
 
* '''Domains:'''  
 
* '''Domains:'''  
−
** substrate binding domain (366–369)
+
** 2 x Dihydroxyacetone phosphate binding domain (210–212), (231–234)
  
−
* '''Modification:''' phosphorylation on Thr-141 AND Ser-259 AND Tyr-281 AND Ser-325 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
+
* '''Modification:''' phosphorylation on Thr-212 AND Thr-234 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
−
* '''Cofactor(s):''' magnesium ion
+
* '''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:''' [[Eno]]-[[PfkA]], [[Eno]]-[[Rny]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
+
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] and membrane associated [http://www.ncbi.nlm.nih.gov/sites/entrez/18763711 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P37869]
+
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P13243]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33900]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37120]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.11]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/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:'''  
−
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''
+
**''fbaA'' [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]
−
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''
+
**''fbaA-[[ywjH]]'' [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''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]
−
''[[cggR]]'': neg. regulated by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed], induced by sugar
 
  
−
''[[pgk]]'': constitutive [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]
+
* '''Regulatory mechanism:'''  
−
 
 
−
* '''Regulatory mechanism:''' transcription repression by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]
 
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 111: Line 109:
 
* '''Mutant:'''  
 
* '''Mutant:'''  
  
−
* '''Expression vector:''' pGP563 (N-terminal His-tag, in [[pWH844]]), pGP93 (N-terminal Strep-tag, for SPINE, in [[pGP380]]), available in [[Stülke]] lab
+
* '''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:''' pHT315-yfp-eno, available in [[Mijakovic]] lab
+
* '''GFP fusion:'''
  
 
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
 
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
  
−
* '''Antibody:''' available in [[Stülke]] lab
+
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Stülke|Jörg Stülke]], University of Göttingen, Germany
 
−
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 130: Line 125:
 
=References=
 
=References=
  
−
# Commichau, F. M., Rothe, F. M., Herzberg, C., Wagner, E., Hellwig, D., Lehnik-Habrink, M., Hammer, E., Völker, U. & Stülke, J. (2009) Novel activities of glycolytic enzymes in Bacillus subtilis: Interactions with essential proteins involved in mRNA processing. Mol. Cell. Proteomics in press [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 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]
−
# Ludwig, H., Homuth, G., Schmalisch, M., Dyka, F. M., Hecker, M., and Stülke, J. (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/sites/entrez/11489127 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]
−
# Jannière, L., Canceill, D., Suski, C., Kanga, S., Dalmais, B., Lestini, R., Monnier, A. F., Chapuis, J., Bolotin, A., Titok, M., Le Chatelier, E., and Ehrlich, S. D. (2007) Genetic evidence for a link between glycolysis and DNA replication. PLoS ONE 2, e447. [http://www.ncbi.nlm.nih.gov/sites/entrez/17505547 PubMed]
 
−
# Leyva-Vazquez, M. A., and Setlow, P. (1994) Cloning and nucleotide sequences of the genes encoding triose phosphate isomerase, phosphoglycerate mutase, and enolase from Bacillus subtilis. J Bacteriol 176: 3903-3910. [http://www.ncbi.nlm.nih.gov/sites/entrez/8021172 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]
 
# 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 15:22, 13 March 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
Gene sequence (+200bp) Protein sequence
Genetic context
FbaA context.gif




The gene

Basic information

  • Coordinates: 3807538 - 3808392

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 = dihydroxyacetone phosphate + D-glyceraldehyde 3-phosphate
  • Protein family: 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:
  • Swiss prot entry: [3]
  • KEGG entry: [4]
  • E.C. number: [5]

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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