Difference between revisions of "Sandbox"

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−
* '''Description:''' pyruvate kinase, glycolytic enzyme <br/><br/>
+
* '''Description:''' alpha-phosphoglucomutase, required for UDP-glucose synthesis <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'''
−
|''pyk''
+
|''pgcA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''pykA''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yhxB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || pyruvate kinase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || alpha-phosphoglucomutase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || interconversion of glucose 6-phosphate and alpha-glucose 1-phosphate
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61,9 kDa, 4.88
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62 kDa, 4.913 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1755 bp, 585 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1695 bp, 565 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pfkA]]'', ''[[ytzA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glpD]]'', ''[[yhcY]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pyk_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yhxB_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pyk_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yhxB_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:pyk_context.gif]]
+
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:yhxB_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 36: Line 38:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 2983830 - 2985584
+
* '''Coordinates:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
Unable to grow with non-PTS carbohydrates (such as glucitol or  glycerol) as single carbon source.
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pfkA-pyk-ytzA.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12661]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10189]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 54: Line 55:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''ADP + phosphoenolpyruvate --> ATP + pyruvate, the reaction is irreversible under physiological conditions
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' pyruvate kinase family, (C-terminal section: PEP-utilizing enzyme family)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylation (Ser36 and Ser535 or 546) [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
+
* '''Modification:''' phosphorylated on ser/thr/tyr [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]  
−
, [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
 
−
* '''Cofactor(s):''' magnesium ion, potassium
 
  
−
* '''Effectors of protein activity:''' activated by PEP [http://www.ncbi.nlm.nih.gov/sites/entrez/4623707 PubMed]
+
* '''Cofactor(s):'''
  
−
* '''Interactions:'''  
+
* '''Effectors of protein activity:'''
  
−
* '''Localization:''' cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
+
* '''Interactions:'''
 +
 
 +
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' 2E28 (from ''Geobacillus stearothermophilus'') [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=62183 NCBI]
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80885]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29180]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU09310]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.40]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[pfkA]] [[pyk]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
+
* '''Operon:'''  
  
 
* '''Sigma factor:'''  
 
* '''Sigma factor:'''  
  
−
* '''Regulation:''' twofold induced by glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
+
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP590 (cat), available in [[Stülke]] lab
+
* '''Mutant:'''
−
 
 
−
* '''Expression vector:'''
 
−
Expression in ''E. coli'', N-terminal His-tag: pGP1100 (in [[pWH844]]), available in [[Stülke]] lab
 
  
−
Expression in ''B. subtilis'', native protein: pGP1411 (in [[pBQ200]]), available in [[Stülke]] lab
+
* '''Expression vector:'''
−
 
+
       
−
Expression in ''B. subtilis'', N-terminal Strep-tag: pGP1409 (in [[pGP380]]), available in [[Stülke]] lab
+
* '''lacZ fusion:'''
−
 
 
−
Expression in ''B. subtilis'', C-terminal Strep-tag: pGP1410 (in [[pGP382]]), available in [[Stülke]] lab
 
−
 
 
−
* '''lacZ fusion:''' see ''[[pfkA]]''
 
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+
* '''two-hybrid system:'''  
  
 
* '''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 131: Line 122:
  
 
# L&#233;vine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. ''Proteomics'' '''6:''' 2157-2173 [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
 
# L&#233;vine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. ''Proteomics'' '''6:''' 2157-2173 [http://www.ncbi.nlm.nih.gov/pubmed/16493705 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]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID 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]
 
−
# Fry, B., Zhu, T., Domach, M. M., Koepsel, R. R., Phalakornkule, C., and Ataai, M. M. (2000) Characterization of growth and acid formation in a Bacillus subtilis pyruvate kinase mutant. Appl Env Microbiol 66: 4045-4049. [http://www.ncbi.nlm.nih.gov/sites/entrez/10966427 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 14:56, 31 March 2009

  • Description: alpha-phosphoglucomutase, required for UDP-glucose synthesis

Gene name pgcA
Synonyms yhxB
Essential no
Product alpha-phosphoglucomutase
Function interconversion of glucose 6-phosphate and alpha-glucose 1-phosphate
MW, pI 62 kDa, 4.913
Gene length, protein length 1695 bp, 565 aa
Immediate neighbours glpD, yhcY
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
YhxB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylated on ser/thr/tyr PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

  1. Lévine et al. (2006) Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6: 2157-2173 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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