Difference between revisions of "Sandbox"

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−
* '''Description:''' aspartokinase II (alpha and beta subunits) <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'''
−
|''lysC''
+
|''pgm''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ask, aecA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''gpmI''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || aspartokinase II (alpha and beta subunits)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of lysine
+
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 4.643 
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56,1 kDa, 5.21
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1224 bp, 408 aa
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1533 bp, 511 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yslB]]'', ''[[ask]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[tpi]]'', ''[[eno]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/lysC_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/lysC_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:lysC_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 31: Line 31:
  
 
<br/><br/>
 
<br/><br/>
 +
  
 
=The gene=
 
=The gene=
Line 36: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Coordinates:''' 3476911 - 3478443
  
 
===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/lysC.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+BG10350]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10898]
  
 
=== 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 = 3-phospho-D-glycerate
  
−
* '''Protein family:'''
+
* '''Protein family:''' BPG-independent phosphoglycerate mutase family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 65: Line 67:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''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:'''
+
* '''Localization:''' Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''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:'''
+
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P39773]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28470]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33910]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.1]
  
 
=== Additional information===
 
=== Additional information===
−
 
+
is pH sensitive
−
:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed], also degraded upon ammonium or amino acid starvation [http://www.ncbi.nlm.nih.gov/sites/entrez/2168395 PubMed]
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
 
* '''Operon:'''  
 
* '''Operon:'''  
 +
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''
 +
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''
 +
 +
* '''Sigma factor:''' [[SigA]]
  
−
* '''Sigma factor:'''  
+
* '''Regulation:''' expression activated by glucose (7.33) [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
  
−
* '''Regulation:''' expression activated by glucose (5.39) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
+
''[[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:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed], also degraded upon ammonium or amino acid starvation [http://www.ncbi.nlm.nih.gov/sites/entrez/2168395 PubMed]
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 105: Line 111:
 
* '''Mutant:'''
 
* '''Mutant:'''
  
−
* '''Expression vector:'''
+
* '''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:'''
  
−
* '''two-hybrid system:'''  
+
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
  
 
* '''Antibody:'''
 
* '''Antibody:'''
  
 
=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=
  
 
=References=
 
=References=
−
hier steht Paper
+
 
−
# M&#228;der et al. (2002) Transcriptome and Proteome Analysis of ''Bacillus subtilis'' Gene Expression Modulated by Amino Acid Availability. ''J. Bacteriol'' '''184:''' 1844288-4295 [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
+
hier kommt Ppaer rein
−
# Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 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]
+
# 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]
 +
# 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]

Revision as of 18:07, 1 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
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: expression activated by glucose (7.33) 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

hier kommt Ppaer rein

  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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