Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
* '''Description:''' triose phosphate isomerase, glycolytic/ gluconeogenic enzyme<br/><br/>
+
* '''Description:''' phosphoglycerate mutase, 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''
+
|''pgm''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''tpiA''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''gpmI''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || triosephosphate isomerase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || 2,3-bisphosphoglycerate-independent <br/>phosphoglycerate mutase
 
|-
 
|-
 
|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''' || 26,9 kDa, 4.79
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56,1 kDa, 5.21
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 759 bp, 253 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1533 bp, 511 amino acids
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pgk]]'', ''[[pgm]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[tpi]]'', ''[[eno]]''
 
|-
 
|-
 
|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:tpi_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:pgm_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 29: Line 29:
 
__TOC__
 
__TOC__
  
<br/><br/>
+
<br/><br/><br/>
  
  
Line 36: Line 36:
 
=== Basic information ===
 
=== Basic information ===
  
* '''Coordinates:''' 3478439 - 3479197
+
* '''Coordinates:''' 3476911 - 3478443
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 46: 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+BG10897]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10898]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
* '''Catalyzed reaction/ biological activity:''' D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate
+
* '''Catalyzed reaction/ biological activity:''' 2-phospho-D-glycerate = 3-phospho-D-glycerate
  
* '''Protein family:''' triosephosphate isomerase family
+
* '''Protein family:''' BPG-independent phosphoglycerate mutase family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 66: Line 66:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
* '''Modification:''' phosphorylation on Ser-213 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
+
* '''Modification:''' phosphorylation on Ser-62 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
  
* '''Cofactor(s):'''
+
* '''Cofactor(s):''' 2 manganese ions per subunit
  
* '''Effectors of protein activity:''' inhibited by 2-phosphoglycolate (in ''B. stearothermophilus'') [http://www.ncbi.nlm.nih.gov/sites/entrez/8580851 PubMed]
+
* '''Effectors of protein activity:''' inhibited by heavy-metal ions, 2,3-butanedione and sulfhydryl agents [http://www.ncbi.nlm.nih.gov/sites/entrez/33963 PubMed]
  
* '''Interactions:'''  
+
* '''Interactions:''' Pgm-[[PfkA]]
  
* '''Localization:''' cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
+
* '''Localization:''' Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
* '''Structure:''' complex with 2-phosphpoglycolic acid, ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=48255 NCBI]
+
* '''Structure:''' ''Geobacillus stearothermophilus'', complex with 2-phosphoglycerate [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=16359 NCBI], ''Geobacillus stearothermophilus'', complex with 3-phosphoglycerate [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=15578 NCBI]
  
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P27876]
+
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P39773]
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33920]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33910]
  
* '''E.C. number:''' [http://www.expasy.org/enzyme/5.3.1.1 5.3.1.1]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.1 5.4.2.1]
  
 
=== Additional information===
 
=== Additional information===
 +
is pH sensitive
  
 
=Expression and regulation=
 
=Expression and regulation=
Line 96: Line 97:
 
* '''Sigma factor:''' [[SigA]]
 
* '''Sigma factor:''' [[SigA]]
  
* '''Regulation:''' expression activated by glucose (2.8 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]   
+
* '''Regulation:''' expression activated by glucose (7.3 fold) [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
+
''[[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]
  
 
* '''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]
 
* '''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]
Line 108: Line 110:
 
* '''Mutant:'''
 
* '''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
+
* '''Expression vector:''' pGP1101 (N-terminal His-tag, in [[pWH844]]), pGP396 (Pgm-S62A, N-terminal His-tag, in [[pWH844]]), pGP92 (N-terminal Strep-tag, for SPINE, expression in B. subtilis, in [[pGP380]]), available in [[Stülke]] lab
 
 
* '''lacZ fusion:'''  
+
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
Line 119: Line 121:
  
 
=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]
 +
 +
[[Jedrzejas|Mark J. Jedrzejas]], Research Center Oakland, CA, USA  [http://www.chori.org/Principal_Investigators/Jedrzejas_Mark_J/jedrzejas_research.html Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 125: Line 131:
  
 
# 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]
+
# 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]
 +
# Meile et al. (2006) Systematic localisation of proteins fused to the green fluorescent protein in ''Bacillus subtilis'': identification of new proteins at the DNA replication factory ''Proteomics'' '''6:''' 2135-2146. [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 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]
+
# 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]
 +
# Ludwig, H., Homuth, G., Schmalisch, M., Dyka, F. M., Hecker, M. & 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]
 +
# Chandler et al. (1999) Structural studies on a 2,3-diphosphoglycerate independent phosphoglycerate mutase from Bacillus stearothermophilus. J. Struct. Biol. 126: 156-165. [http://www.ncbi.nlm.nih.gov/sites/entrez/10388626 PubMed]
 +
# Jedrzejas et al. (2000) Structure and mechanism of action of a novel phosphoglycerate mutase from Bacillus stearothermophilus. EMBO J. 19: 1419-1431. [http://www.ncbi.nlm.nih.gov/sites/entrez/10747010 PubMed]
 +
# Jedrzejas et al. (2000) Mechanism of catalysis of the cofactor-independent phosphoglycerate mutase from Bacillus stearothermophilus. Crystal structure of the complex with a 2-phosphoglycerate. J. Biol. Chem. 275: 23146-23153. [http://www.ncbi.nlm.nih.gov/sites/entrez/10764795 PubMed]
 +
# Jedrzejas and Setlow (2001)  Comparison of the binuclear metalloenzymes diphosphoglycerate-independent phosphoglycerate mutase and alkaline phosphatase: their mechanism of catalysis via a phosphoserine intermediate. Chem. Rev. 101: 607-618. [http://www.ncbi.nlm.nih.gov/sites/entrez/11712498 PubMed]
 +
# Ridgen et al. (2003) Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography, simulated dynamics and molecular modeling. J. Mol. Biol. 328: 909-920. [http://www.ncbi.nlm.nih.gov/sites/entrez/12729763 PubMed]
 +
# Nukui et al. (2007) Structure and molecular mechanism of Bacillus anthracis cofactor-independent phosphoglycerate mutase: a crucial enzyme for spores and growing cells of Bacillus species. Biophys. J. 92: 977-988. [http://www.ncbi.nlm.nih.gov/sites/entrez/17085493 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: phosphoglycerate mutase, glycolytic/ gluconeogenic enzyme

Gene name pgm
Synonyms gpmI
Essential yes
Product 2,3-bisphosphoglycerate-independent
phosphoglycerate mutase
Function enzyme in glycolysis/ gluconeogenesis
MW, pI 56,1 kDa, 5.21
Gene length, protein length 1533 bp, 511 amino acids
Immediate neighbours tpi, eno
Hier soll was neues rein
Genetic context
Pgm context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Coordinates: 3476911 - 3478443

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 = 3-phospho-D-glycerate
  • Protein family: BPG-independent phosphoglycerate mutase family
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Cofactor(s): 2 manganese ions per subunit
  • Effectors of protein activity: inhibited by heavy-metal ions, 2,3-butanedione and sulfhydryl agents PubMed
  • Interactions: Pgm-PfkA
  • Localization: Cytoplasm (Homogeneous) PubMed

Database entries

  • Structure: Geobacillus stearothermophilus, complex with 2-phosphoglycerate NCBI, Geobacillus stearothermophilus, complex with 3-phosphoglycerate NCBI
  • Swiss prot entry: [3]
  • KEGG entry: [4]

Additional information

is pH sensitive

Expression and regulation

  • Regulation: expression activated by glucose (7.3 fold) 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: pGP1101 (N-terminal His-tag, in pWH844), pGP396 (Pgm-S62A, N-terminal His-tag, in pWH844), pGP92 (N-terminal Strep-tag, for SPINE, expression in B. subtilis, in pGP380), 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

Jörg Stülke, University of Göttingen, Germany Homepage

Mark J. Jedrzejas, Research Center Oakland, CA, USA 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. Meile et al. (2006) Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory Proteomics 6: 2135-2146. PubMed
  4. 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
  5. 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
  6. Ludwig, H., Homuth, G., Schmalisch, M., Dyka, F. M., Hecker, M. & 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
  7. Chandler et al. (1999) Structural studies on a 2,3-diphosphoglycerate independent phosphoglycerate mutase from Bacillus stearothermophilus. J. Struct. Biol. 126: 156-165. PubMed
  8. Jedrzejas et al. (2000) Structure and mechanism of action of a novel phosphoglycerate mutase from Bacillus stearothermophilus. EMBO J. 19: 1419-1431. PubMed
  9. Jedrzejas et al. (2000) Mechanism of catalysis of the cofactor-independent phosphoglycerate mutase from Bacillus stearothermophilus. Crystal structure of the complex with a 2-phosphoglycerate. J. Biol. Chem. 275: 23146-23153. PubMed
  10. Jedrzejas and Setlow (2001) Comparison of the binuclear metalloenzymes diphosphoglycerate-independent phosphoglycerate mutase and alkaline phosphatase: their mechanism of catalysis via a phosphoserine intermediate. Chem. Rev. 101: 607-618. PubMed
  11. Ridgen et al. (2003) Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography, simulated dynamics and molecular modeling. J. Mol. Biol. 328: 909-920. PubMed
  12. Nukui et al. (2007) Structure and molecular mechanism of Bacillus anthracis cofactor-independent phosphoglycerate mutase: a crucial enzyme for spores and growing cells of Bacillus species. Biophys. J. 92: 977-988. PubMed
  13. Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed