Difference between revisions of "Sandbox"

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−
* '''Description:''' unknown <br/><br/>
+
* '''Description:''' enolase, 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'''
−
|''yonV''
+
|''eno''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || enolase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 9.447 
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46,4 kDa, 4.49
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1230 bp, 410 aa
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1290 bp, 430 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yonX]]'', ''[[yonU]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pgm]]'', ''[[yvgK]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yonV_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|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/yonV_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/eno_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yonV_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:eno_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>
 
|-
 
|-
Line 31: Line 31:
  
 
<br/><br/>
 
<br/><br/>
 +
  
 
=The gene=
 
=The gene=
Line 36: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Coordinates:''' 3475589 - 3476878
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential  [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13632]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10899]
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=The protein=
 
=The protein=
Line 53: Line 55:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' 2-phospho-D-glycerate = phosphoenolpyruvate + H(2)O
  
−
* '''Protein family:'''
+
* '''Protein family:''' enolase family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 64: Line 66:
  
 
* '''Domains:'''  
 
* '''Domains:'''  
 +
** substrate binding domain (366–369)
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylation on Thr-141 AND Ser-259 AND Tyr-281 AND Ser-325 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
  
−
* '''Cofactor(s):'''
+
* '''Cofactor(s):''' magnesium ion
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[Eno]]-[[PfkA]], [[Eno]]-[[Rny]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
  
−
* '''Localization:'''
+
* '''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]
  
 
=== Database entries ===
 
=== Database entries ===
Line 79: Line 82:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P37869]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU20980]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33900]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.11]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=Expression and regulation=
 
=Expression and regulation=
  
 
* '''Operon:'''  
 
* '''Operon:'''  
 +
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''
 +
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''
  
−
* '''Sigma factor:'''  
+
* '''Sigma factor:''' [[SigA]]
  
−
* '''Regulation:''' expression activated by glucose (3.27) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], induced by glucose (3-fold: [[CcpA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed]
+
* '''Regulation:''' expression activated by glucose (3.28) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 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
  
−
* '''Regulatory mechanism:''' [[CcpA]]: mechanism unknown [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed]  
+
''[[pgk]]'': constitutive [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]
 +
 
 +
* '''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 101: Line 110:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:'''  
  
−
* '''Expression vector:'''
+
* '''Expression vector:''' pGP563 (N-terminal His-tag, in [[pWH844]]), pGP93 (N-terminal Strep-tag, for SPINE, in [[pGP380]]), available in [[Stülke]] lab
−
       
+
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
−
* '''GFP fusion:'''
+
* '''GFP fusion:''' pHT315-yfp-eno, available in [[Mijakovic]] lab
  
−
* '''two-hybrid system:'''  
+
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
  
−
* '''Antibody:'''
+
* '''Antibody:''' available in [[Stülke]] lab
  
 
=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 119: Line 131:
 
=References=
 
=References=
  
−
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
+
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
−
# Blencke, H.-M., Homuth, G., Ludwig, H., Mäder, U., Hecker, M. & Stülke, J. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab. Engn. 5: 133-149. [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed]
+
# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. ''Proteomics'' '''7:''' 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
# L&#233;vine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. ''Proteomics'' '''6:''' 2157-2173 [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
 +
# 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]
 +
# 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]
 +
# 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]

Revision as of 22:28, 1 April 2009

  • Description: enolase, glycolytic/ gluconeogenic enzyme

Gene name eno
Synonyms
Essential yes
Product enolase
Function enzyme in glycolysis/ gluconeogenesis
MW, pI 46,4 kDa, 4.49
Gene length, protein length 1290 bp, 430 amino acids
Immediate neighbours pgm, yvgK
Gene sequence (+200bp) Protein sequence
Genetic context
Eno context.gif
This image was kindly provided by SubtiList




The gene

Basic information

  • Coordinates: 3475589 - 3476878

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: 2-phospho-D-glycerate = phosphoenolpyruvate + H(2)O
  • Protein family: enolase family
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
    • substrate binding domain (366–369)
  • Modification: phosphorylation on Thr-141 AND Ser-259 AND Tyr-281 AND Ser-325 PubMed, PubMed, PubMed
  • Cofactor(s): magnesium ion
  • Effectors of protein activity:
  • Localization: cytoplasm PubMed and membrane associated PubMed

Database entries

  • Structure:
  • Swiss prot entry: [3]
  • KEGG entry: [4]
  • E.C. number: [5]

Additional information

Expression and regulation

  • Regulation: expression activated by glucose (3.28) PubMed

cggR: neg. regulated by CggR PubMed, induced by sugar

pgk: constitutive PubMed

  • Regulatory mechanism: transcription repression by CggR PubMed
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector: pGP563 (N-terminal His-tag, in pWH844), pGP93 (N-terminal Strep-tag, for SPINE, in pGP380), available in Stülke lab
  • lacZ fusion:
  • GFP fusion: pHT315-yfp-eno, available in Mijakovic lab
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab
  • Antibody: available in Stülke lab

Labs working on this gene/protein

Jörg Stülke, University of Göttingen, Germany Homepage

Your additional remarks

References

  1. Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab Eng 5: 133-149 PubMed
  2. Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis. Proteomics 7: 3509-3526. PubMed
  3. Lévine et al. (2006) Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6: 2157-2173 PubMed
  4. 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 PubMed
  5. 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.PubMed
  6. 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. PubMed
  7. 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. PubMed
  8. 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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