Difference between revisions of "Sandbox"

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−
* '''Description:''' phosphofructokinase, glycolytic enzyme <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'''
−
|''pfkA''
+
|''pyk''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''pfk''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''pykA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || 6-phosphofructokinase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || pyruvate kinase
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
 
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34,1 kDa, 6.14
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61,9 kDa, 4.88
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 957 bp, 319 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1755 bp, 585 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[accA]]'', ''[[pyk]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pfkA]]'', ''[[ytzA]]''
 
|-
 
|-
 
|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:pfkA_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 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 2985630 - 2986586
+
* '''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 ===
Line 45: Line 45:
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pfkA-pyk-ytzA.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pfkA-pyk-ytzA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12644]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12661]
  
 
=== Additional information===
 
=== Additional information===
Line 53: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6-bisphosphate
+
* '''Catalyzed reaction/ biological activity:'''ADP + phosphoenolpyruvate --> ATP + pyruvate, the reaction is irreversible under physiological conditions
  
−
* '''Protein family:''' phosphofructokinase family
+
* '''Protein family:''' pyruvate kinase family, (C-terminal section: PEP-utilizing enzyme family)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 64: Line 64:
  
 
* '''Domains:'''  
 
* '''Domains:'''  
−
** 3 x nucleotide binding domain (ATP) (21–25), (154–158), (171–187)
 
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylation on Ser36 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], phosphorylation on Ser536 or Ser546 [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
  
−
* '''Cofactor(s):''' ATP
+
* '''Cofactor(s):''' magnesium ion, potassium
  
−
* '''Effectors of protein activity:''' inhibited by citrate, ATP, PEP, Ca2+, and others (in ''B. licheniformes'') [http://www.ncbi.nlm.nih.gov/pubmed/4269800 PubMed]
+
* '''Effectors of protein activity:''' activated by PEP [http://www.ncbi.nlm.nih.gov/sites/entrez/4623707 PubMed]
  
−
* '''Interactions:''' [[PfkA]]-[[Pgm]], [[PfkA]]-[[Eno]], [[PfkA]]-[[Rny]], [[PfkA]]-[[PnpA]], [[PfkA]]-[[RnjA]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
+
* '''Interactions:'''  
  
−
* '''Localization:''' Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
+
* '''Localization:''' cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=58449 NCBI], Mutant form, complex with fructose-6-phosphate ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=21480 NCBI]
+
* '''Structure:''' 2E28 (from ''Geobacillus stearothermophilus'') [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=62183 NCBI]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34529]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80885]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29190]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29180]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.11 2.7.1.11]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.40 2.7.1.40]
  
 
=== Additional information===
 
=== Additional information===
Line 91: Line 90:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''pfkA [[pyk]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
+
* '''Operon:''' ''[[pfkA]] [[pyk]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
  
 
* '''Sigma factor:'''  
 
* '''Sigma factor:'''  
Line 103: Line 102:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' GP590 (cat), available in [[Stülke]] lab
  
−
* '''Expression vector:''' pGP393 (N-terminal His-tag, in [[pWH844]]), pGP87 (N-terminal Strep-tag, for SPINE, expression in ''B. subtilis'', in [[pGP380]]), available in [[Stülke]] lab
+
* '''Expression vector:'''  
−
+
Expression in ''E. coli'', N-terminal His-tag: pGP1100 (in [[pWH844]]), available in [[Stülke]] lab
−
* '''lacZ fusion:''' pGP511 (in [[pAC6]]), 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:'''
 
* '''GFP fusion:'''
Line 123: Line 129:
 
=References=
 
=References=
  
−
# 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]
+
# 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]
−
# Commichau, F. M., Rothe, F. M., Herzberg, C., Wagner, E., Hellwig, D., Lehnik-Habrink, M., Hammer, E., Völker, U. & Stülke, J. (2009) Novel activities of glycolytic enzymes in Bacillus subtilis: Interactions with essential proteins involved in mRNA processing. Mol. Cell. Proteomics in press [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 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]
+
# 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 18:18, 15 April 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
Hier soll was neues rein
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 on Ser36 PubMed, PubMed, phosphorylation on Ser536 or Ser546 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]

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. Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis. Proteomics 7: 3509-3526. PubMed
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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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