Difference between revisions of "Sandbox"

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−
* '''Description:''' 6-phosphogluconate dehydrogenase <br/><br/>
+
* '''Description:''' triose phosphate isomerase, 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'''
−
|''gntZ''
+
|''tpi''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''tpiA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || 6-phosphogluconate dehydrogenase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || triosephosphate isomerase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || gluconate utilization
+
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 51 kDa, 4.756 
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26,9 kDa, 4.79
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1404 bp, 468 aa
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 759 bp, 253 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gntP]]'', ''[[ahpC]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pgk]]'', ''[[pgm]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gntZ_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/tpi_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gntZ_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/tpi_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:gntZ_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:tpi_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 36: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Coordinates:''' 3478439 - 3479197
  
 
===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/gntRKPZ.html]
+
* '''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+BG10651]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10897]
  
 
=== 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:''' D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate
  
−
* '''Protein family:'''
+
* '''Protein family:''' triosephosphate isomerase family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylation on Ser-213 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:'''
+
* '''Effectors of protein activity:''' inhibited by 2-phosphoglycolate (in ''B. stearothermophilus'') [http://www.ncbi.nlm.nih.gov/sites/entrez/8580851 PubMed]
  
−
* '''Interactions:'''
+
* '''Interactions:'''  
  
−
* '''Localization:'''
+
* '''Localization:''' cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' complex with 2-phosphpoglycolic acid, ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=48255 NCBI]
  
−
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P27876]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40080]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33920]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/5.3.1.1]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[gntR]]-[[gntK]]-[[gntP]]-[[gntZ]]''
+
* '''Operon:'''  
 +
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''
 +
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''
  
 
* '''Sigma factor:''' [[SigA]]
 
* '''Sigma factor:''' [[SigA]]
  
−
* '''Regulation:''' expression activated by glucose (2.57) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]   
+
* '''Regulation:''' expression activated by glucose (2.77) [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
 +
 
 +
''[[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 103: Line 110:
 
* '''Mutant:'''
 
* '''Mutant:'''
  
−
* '''Expression vector:'''
+
* '''Expression vector:''' pGP394 (N-terminal His-tag, in [[pWH844]]), pGP89 (N-terminal Strep-tag, for SPINE, expression in B. subtilis), available in [[Stülke]] lab
−
       
+
−
* '''lacZ fusion:'''
+
* '''lacZ fusion:'''  
  
 
* '''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 120: Line 127:
  
 
# 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]
−
# Fujita Y, Fujita T, Miwa Y, Nihashi J, Aratani Y. (1986) Organization and transcription of the gluconate operon, gnt, of Bacillus subtilis. ''J Biol Chem.'' '''Oct 15;261(29):''' 13744-53. [http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 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]
−
# Reizer A., Deutscher J., Saier M.H. Jr., Reizer J. (1991) Analysis of the gluconate (gnt) operon of Bacillus subtilis. ''Mol. Microbiol.'' '''5:''' 1081-1089. [http://www.ncbi.nlm.nih.gov/sites/entrez/1659648 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]
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID 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: triose phosphate isomerase, glycolytic/ gluconeogenic enzyme

Gene name tpi
Synonyms tpiA
Essential yes
Product triosephosphate isomerase
Function enzyme in glycolysis/ gluconeogenesis
MW, pI 26,9 kDa, 4.79
Gene length, protein length 759 bp, 253 amino acids
Immediate neighbours pgk, pgm
Gene sequence (+200bp) Protein sequence
Genetic context
Tpi context.gif
This image was kindly provided by SubtiList




The gene

Basic information

  • Coordinates: 3478439 - 3479197

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-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate
  • Protein family: triosephosphate isomerase family
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylation on Ser-213 PubMed
  • Cofactor(s):
  • Effectors of protein activity: inhibited by 2-phosphoglycolate (in B. stearothermophilus) PubMed
  • Interactions:
  • Localization: cytoplasm PubMed

Database entries

  • Structure: complex with 2-phosphpoglycolic acid, Geobacillus stearothermophilus NCBI
  • Swiss prot entry: [3]
  • KEGG entry: [4]
  • E.C. number: [5]

Additional information

Expression and regulation

  • Regulation: expression activated by glucose (2.77) 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: pGP394 (N-terminal His-tag, in pWH844), pGP89 (N-terminal Strep-tag, for SPINE, expression in B. subtilis), available in Stülke lab
  • lacZ fusion:
  • 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. 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. 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
  3. 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
  4. 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
  5. 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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