Difference between revisions of "Sandbox"
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| − | * '''Description:''' | + | * '''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''' | ||
| − | |'' | + | |''tpi'' |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' '' | + | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''tpiA'' |
|- | |- | ||
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes | |style="background:#ABCDEF;" align="center"| '''Essential''' || yes | ||
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''Product''' || | + | |style="background:#ABCDEF;" align="center"| '''Product''' || triosephosphate isomerase |
|- | |- | ||
|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''' || | + | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26,9 kDa, 4.79 |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || | + | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 759 bp, 253 amino acids |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ | + | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pgk]]'', ''[[pgm]]'' |
|- | |- | ||
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein''' | |colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein''' | ||
|- | |- | ||
| − | |colspan="2" | '''Genetic context''' <br/> [[Image: | + | |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= | ||
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=== Basic information === | === Basic information === | ||
| − | * '''Coordinates:''' | + | * '''Coordinates:''' 3478439 - 3479197 |
===Phenotypes of a mutant === | ===Phenotypes of a mutant === | ||
| − | essential | + | essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed] |
=== Database entries === | === Database entries === | ||
| Line 45: | Line 46: | ||
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.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+ | + | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10897] |
=== Additional information=== | === Additional information=== | ||
| Line 53: | Line 54: | ||
=== 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):''' | ||
| Line 64: | Line 65: | ||
* '''Domains:''' | * '''Domains:''' | ||
| − | |||
| − | |||
| − | * '''Modification:''' phosphorylation on Ser- | + | * '''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:''' ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid= | + | * '''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:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac? | + | * '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P27876] |
| − | * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+ | + | * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33920] |
| − | * '''E.C. number:''' [http://www.expasy.org/enzyme/ | + | * '''E.C. number:''' [http://www.expasy.org/enzyme/5.3.1.1 5.3.1.1] |
=== Additional information=== | === Additional information=== | ||
| − | |||
=Expression and regulation= | =Expression and regulation= | ||
| Line 99: | Line 97: | ||
* '''Regulation:''' expression activated by glucose (2.8 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed] | * '''Regulation:''' expression activated by glucose (2.8 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed] | ||
| − | **''[[cggR]]'': | + | **''[[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] | **''[[pgk]]'': constitutive [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed] | ||
| Line 110: | Line 108: | ||
* '''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:''' | ||
| Line 127: | Line 125: | ||
# 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] | ||
| − | |||
| − | |||
# 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., 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] | # 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 17:44, 15 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 |
| Hier soll was neues rein | |
Genetic context 
This image was kindly provided by SubtiList
| |
Contents
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: 5.3.1.1
Additional information
Expression and regulation
- Sigma factor: SigA
- Regulation: expression activated by glucose (2.8 fold) 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
- 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
- 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
- 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
- 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
- Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
