Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' serine hydroxymethyltransferase <br/><br/>
+
* '''Description:''' pyruvate kinase, glycolytic 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'''
−
|''glyA''
+
|''pyk''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''glyC, ipc-34d ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''pykA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || serine hydroxymethyltransferase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || pyruvate kinase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of glycine
+
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 5.475 
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61,9 kDa, 4.88
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1245 bp, 415 aa
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1755 bp, 585 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[upp]]'', ''[[ywlG]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pfkA]]'', ''[[ytzA]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/glyA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|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/glyA_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pyk_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:glyA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:pyk_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 36:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Coordinates:''' 2983830 - 2985584
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
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/glyA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pfkA-pyk-ytzA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10944]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12661]
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=The protein=
 
=The protein=
Line 55: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:'''ADP + phosphoenolpyruvate --> ATP + pyruvate, the reaction is irreversible under physiological conditions
  
−
* '''Protein family:'''
+
* '''Protein family:''' pyruvate kinase family, (C-terminal section: PEP-utilizing enzyme family)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 67: Line 66:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylated on ser/thr/tyr [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]  
+
* '''Modification:''' phosphorylation (Ser36 and Ser535 or 546) [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
 +
, [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
  
−
* '''Cofactor(s):'''
+
* '''Cofactor(s):''' magnesium ion, potassium
  
−
* '''Effectors of protein activity:'''
+
* '''Effectors of protein activity:''' activated by PEP [http://www.ncbi.nlm.nih.gov/sites/entrez/4623707 PubMed]
  
−
* '''Interactions:'''
+
* '''Interactions:'''  
  
−
* '''Localization:'''
+
* '''Localization:''' cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' 2E28 (from ''Geobacillus stearothermophilus'') [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=62183 NCBI]
  
−
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80885]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU36900]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29180]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.40]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[glyA]]''
+
* '''Operon:''' ''[[pfkA]] [[pyk]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''Sigma factor:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' twofold induced by glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
Line 103: Line 104:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' GP590 (cat), available in [[Stülke]] lab
 +
 
 +
* '''Expression vector:'''
 +
Expression in ''E. coli'', N-terminal His-tag: pGP1100 (in [[pWH844]]), available in [[Stülke]] lab
  
−
* '''Expression vector:'''
+
Expression in ''B. subtilis'', native protein: pGP1411 (in [[pBQ200]]), available in [[Stülke]] lab
−
       
+
 
−
* '''lacZ fusion:'''
+
Expression in ''B. subtilis'', N-terminal Strep-tag: pGP1409 (in [[pGP380]]), available in [[Stülke]] lab
 +
 
 +
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:'''  
+
* '''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 122: Line 132:
  
 
# 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]
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID 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]
 +
# 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 14:53, 31 March 2009

  • Description: pyruvate kinase, glycolytic enzyme

Gene name pyk
Synonyms pykA
Essential no
Product pyruvate kinase
Function catabolic enzyme in glycolysis
MW, pI 61,9 kDa, 4.88
Gene length, protein length 1755 bp, 585 amino acids
Immediate neighbours pfkA, ytzA
Gene sequence (+200bp) Protein sequence
Genetic context
Pyk context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates: 2983830 - 2985584

Phenotypes of a mutant

Unable to grow with non-PTS carbohydrates (such as glucitol or glycerol) as single carbon source.

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:ADP + phosphoenolpyruvate --> ATP + pyruvate, the reaction is irreversible under physiological conditions
  • Protein family: pyruvate kinase family, (C-terminal section: PEP-utilizing enzyme family)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylation (Ser36 and Ser535 or 546) PubMed

, PubMed

  • Cofactor(s): magnesium ion, potassium
  • Effectors of protein activity: activated by PEP PubMed
  • Interactions:
  • Localization: cytoplasm PubMed

Database entries

  • Structure: 2E28 (from Geobacillus stearothermophilus) NCBI
  • Swiss prot entry: [3]
  • KEGG entry: [4]
  • E.C. number: [5]

Additional information

Expression and regulation

  • Sigma factor:
  • Regulation: twofold induced by glucose PubMed
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant: GP590 (cat), available in Stülke lab
  • 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 in B. subtilis, N-terminal Strep-tag: pGP1409 (in pGP380), available in Stülke lab

Expression in B. subtilis, C-terminal Strep-tag: pGP1410 (in pGP382), available in Stülke lab

  • lacZ fusion: see pfkA
  • 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. 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. 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
  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. 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. PubMed
  5. Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=46056"