Difference between revisions of "Sandbox"

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−
* '''Description:''' unknown <br/><br/>
+
* '''Description:''' glucose 6-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'''
−
|''yugE''
+
|''pgi''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yugL ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || glucose-6-phosphate isomerase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 9 kDa, 4.136 
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50.4 kDa, 4.85
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 264 bp, 88 aa
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1353 bp, 451 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yugF]]'', ''[[patB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yugM]]'', ''[[yugK]]''
 
|-
 
|-
 
|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:yugE_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:pgi_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 31:
 
__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 35: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Coordinates:''' 3219772 - 3221124
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yugE.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pgi-yugMN.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12359]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12366]
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=The protein=
 
=The protein=
Line 52: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' D-glucose 6-phosphate = D-fructose 6-phosphate
  
−
* '''Protein family:'''
+
* '''Protein family:''' GPI family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 64: Line 65:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylation on Thr-39 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:'''
+
* '''Effectors of protein activity:''' inhibited by 6-phosphogluconate (in ''B.caldotenax, B.stearothermophilus'') [http://www.ncbi.nlm.nih.gov/pubmed/7400125 PubMed]
  
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' cytoplasm
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=54052 NCBI], ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=11544 NCBI]
  
−
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80860]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU31430]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU31350]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/5.3.1.9 5.3.1.9]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''pgi'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' constitutively expressed [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
  
−
* '''Regulatory mechanism:'''
+
* '''Additional information:'''
−
 
 
−
* '''Additional information:'''  
 
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' GP508 (spc), available in [[Stülke]] lab
  
−
* '''Expression vector:'''
+
* '''Expression vector:''' pGP762 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
−
       
+
−
* '''lacZ fusion:'''
+
* '''lacZ fusion:''' pGP510 (in [[pAC6]]), available in [[Stülke]] lab
  
 
* '''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]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 118: Line 120:
 
=References=
 
=References=
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID 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]
 +
# Lee et al. (2008) Crystallization and preliminary crystallographic study of the phosphoglucose isomerase from Bacillus subtilis. Acta Cryst. Sect. F 64:1181-1183. [http://www.ncbi.nlm.nih.gov/sites/entrez/19052382 PubMed]
 +
# Lin and Prasad (1975) Selection of a mutant of Bacillus subtilis deficient in glucose-6-phosphate dehydrogenase and phosphoglucoisomerase. J. Gen. Microbiol. 83:419-421. [http://www.ncbi.nlm.nih.gov/sites/entrez/4214896 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]
 +
# Prasad and Freese (1974) Cell lysis of Bacillus subtilis caused by intracellular accumulation of glucose-1-phosphate. J. Bacteriol. 118:1111-1122. [http://www.ncbi.nlm.nih.gov/sites/entrez/4275311 PubMed]
 +
# Stülke, J., Martin-Verstraete, I., Glaser, P. & Rapoport, G. (2001) Characterization of glucose repression resistant mutants of Bacillus subtilis: identification of the glcR gene. Arch. Microbiol. 175: 441-449. [http://www.ncbi.nlm.nih.gov/sites/entrez/11491085 PubMed]
 +
# Macek et al. (2007) The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis. ''Mol Cell Proteomics'' '''6(4):''' 697-707. [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

Revision as of 15:02, 15 April 2009

  • Description: glucose 6-phosphate isomerase, glycolytic/ gluconeogenic enzyme

Gene name pgi
Synonyms yugL
Essential no
Product glucose-6-phosphate isomerase
Function enzyme in glycolysis/ gluconeogenesis
MW, pI 50.4 kDa, 4.85
Gene length, protein length 1353 bp, 451 amino acids
Immediate neighbours yugM, yugK
Hier soll was neues rein
Genetic context
Pgi context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Coordinates: 3219772 - 3221124

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: D-glucose 6-phosphate = D-fructose 6-phosphate
  • Protein family: GPI family
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylation on Thr-39 PubMed
  • Cofactor(s):
  • Effectors of protein activity: inhibited by 6-phosphogluconate (in B.caldotenax, B.stearothermophilus) PubMed
  • Interactions:
  • Localization: cytoplasm

Database entries

  • Structure: Geobacillus stearothermophilus NCBI, Geobacillus stearothermophilus NCBI
  • Swiss prot entry: [3]
  • KEGG entry: [4]

Additional information

Expression and regulation

  • Sigma factor:
  • Regulation: constitutively expressed PubMed
  • Additional information:

Biological materials

  • Mutant: GP508 (spc), available in Stülke lab
  • Expression vector: pGP762 (N-terminal His-tag, in pWH844), available in Stülke lab
  • lacZ fusion: pGP510 (in pAC6), available in Stülke lab
  • 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

Your additional remarks

References

  1. Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
  2. Lee et al. (2008) Crystallization and preliminary crystallographic study of the phosphoglucose isomerase from Bacillus subtilis. Acta Cryst. Sect. F 64:1181-1183. PubMed
  3. Lin and Prasad (1975) Selection of a mutant of Bacillus subtilis deficient in glucose-6-phosphate dehydrogenase and phosphoglucoisomerase. J. Gen. Microbiol. 83:419-421. PubMed
  4. 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
  5. Prasad and Freese (1974) Cell lysis of Bacillus subtilis caused by intracellular accumulation of glucose-1-phosphate. J. Bacteriol. 118:1111-1122. PubMed
  6. Stülke, J., Martin-Verstraete, I., Glaser, P. & Rapoport, G. (2001) Characterization of glucose repression resistant mutants of Bacillus subtilis: identification of the glcR gene. Arch. Microbiol. 175: 441-449. PubMed
  7. Macek et al. (2007) The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol Cell Proteomics 6(4): 697-707. PubMed
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