Difference between revisions of "Sandbox"

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−
* '''Description:''' phosphoglycerate kinase, 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'''
−
|''pgk''
+
|''pgm''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|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''' || phosphoglycerate kinase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || 2,3-bisphosphoglycerate-independent 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''' || 42,0 kDa, 4.77
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56,1 kDa, 5.21
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1182 bp, 394 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1533 bp, 511 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gapA]]'', ''[[tpi]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[tpi]]'', ''[[eno]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pgk_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pgm_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pgk_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pgm_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:pgk_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>
 
|-
 
|-
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<br/><br/>
 
<br/><br/>
 +
  
 
=The gene=
 
=The gene=
Line 36: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 3479231 - 3480412
+
* '''Coordinates:''' 3476911 - 3478443
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 46: Line 47:
 
* '''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+BG11062]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10898]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 55:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' ATP + 3-phospho-D-glycerate = ADP + 1,3-bisphosphoglycerate
+
* '''Catalyzed reaction/ biological activity:''' 2-phospho-D-glycerate = 3-phospho-D-glycerate
  
−
* '''Protein family:''' phosphoglycerate kinase family
+
* '''Protein family:''' BPG-independent phosphoglycerate mutase family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
−
** nucleotide binding domain (ATP) (350–353)
 
−
** 2x substrate binding domain (21–23), (59–62)
 
  
−
* '''Modification:''' phosphorylation on Ser-183 AND Thr-299 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 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:'''
+
* '''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 (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
 
* '''Localization:''' Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
Line 80: Line 79:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=57113 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?P40924]
+
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P39773]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33930]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33910]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.2.3]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.1]
  
 
=== Additional information===
 
=== Additional information===
−
 
+
is pH sensitive
  
 
=Expression and regulation=
 
=Expression and regulation=
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* '''Mutant:'''
 
* '''Mutant:'''
  
−
* '''Expression vector:''' pGP1102 (N-terminal His-tag, in [[pWH844]]), pGP95 (N-terminal Strep-tag, in [[pGP172]]), pGP91 (N-terminal Strep-tag, for SPINE, expression in ''B. subtilis'', in [[pGP380]]), 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:''' pGP514 (in [[pAC6]]), a series of promoter deletion variants is also available in [[pAC6]], available in [[Stülke]] lab
+
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
Line 123: Line 122:
  
 
=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 130: Line 133:
 
# 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]
 
# 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]
 
# 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]
−
# 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]
 +
# 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 16:10, 31 March 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
Gene sequence (+200bp) Protein sequence
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]
  • E.C. number: [5]

Additional information

is pH sensitive

Expression and regulation

  • Regulation:

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. Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis. Proteomics 7: 3509-3526. PubMed
  2. 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
  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. 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
  6. Chandler et al. (1999) Structural studies on a 2,3-diphosphoglycerate independent phosphoglycerate mutase from Bacillus stearothermophilus. J. Struct. Biol. 126: 156-165. PubMed
  7. Jedrzejas et al. (2000) Structure and mechanism of action of a novel phosphoglycerate mutase from Bacillus stearothermophilus. EMBO J. 19: 1419-1431. PubMed
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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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