Difference between revisions of "Sandbox"

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−
* '''Description:''' phosphoribosylformylglycinamidine synthase <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'''
−
|''purQ''
+
|''pyk''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''pykA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoribosylformylglycinamidine synthase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || pyruvate kinase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || purine biosynthesis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 24 kDa, 4.627 
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61,9 kDa, 4.88
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 681 bp, 227 aa
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1755 bp, 585 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[purS]]'', ''[[purL]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pfkA]]'', ''[[ytzA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12467&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14878&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:pyk_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:purQ_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 37: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU06470
+
* '''Locus tag:''' BSU29180
  
 
===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/purEKBCSQLFMNHD.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pfkA-pyk-ytzA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10706]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12661]
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=The protein=
 
=The protein=
Line 54: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' ATP + N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide + L-glutamine + H<sub>2</sub>O = ADP + phosphate + 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine + L-glutamate (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:''' ADP + phosphoenolpyruvate --> ATP + pyruvate, the reaction is irreversible under physiological conditions
  
−
* '''Protein family:'''
+
* '''Protein family:''' PEP-utilizing enzyme family (according to Swiss-Prot) pyruvate kinase family, (C-terminal section: PEP-utilizing enzyme family)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 66: Line 65:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''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):'''
+
* '''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:''' [[PurS]]-[[PurQ]]-[[PurL]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15301530 PubMed]
+
* '''Interactions:'''  
  
−
* '''Localization:''' cytoplasm (according to Swiss-Prot)
+
* '''Localization:''' cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2E28 2E28] (Geobacillus stearothermophilus), 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/P12041 P12041]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80885]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU06470]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29180]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/6.3.5.3 6.3.5.3]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.40 2.7.1.40]
  
 
=== Additional information===
 
=== 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]
+
 
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[purE]]-[[purK]]-[[purB]]-[[purC]]-[[purS]]-[[purQ]]-[[purL]]-[[purF]]-[[purM]]-[[purN]]-[[purH]]-[[purD]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3036807 PubMed]
+
* '''Operon:''' ''[[pfkA]] [[pyk]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/3036807 PubMed]
+
* '''Sigma factor:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' twofold induced by glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
−
** repressed in the presence of adenine or adenosine([[PurR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/2536750 PubMed]
 
−
** repressed in the presence of guanine([[G-box]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/3036807 PubMed]
 
−
** expression activated by glucose (4.4 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
 
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
−
** [[PurR]]: transcription repression (molecular inducer: PRPP) [http://www.ncbi.nlm.nih.gov/sites/entrez/2536750 PubMed]
 
−
** [[G-box]]: transcription termination/ antitermination ([[riboswitch]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/3036807 PubMed1] [http://www.ncbi.nlm.nih.gov/sites/entrez/12787499 PubMed2]
 
  
−
* '''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]
+
* '''Additional information:'''
  
 
=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 126: Line 129:
 
=References=
 
=References=
  
−
<pubmed>12850135, </pubmed>
+
<pubmed>17726680 16493705 11489127 17505547 10966427 17218307, </pubmed>
−
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 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]
−
# 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]
+
# 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 13:31, 8 June 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
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
Pyk context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU29180

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: PEP-utilizing enzyme family (according to Swiss-Prot) 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 (Geobacillus stearothermophilus), 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

Christine Eymann, Dörte Becher, Jörg Bernhardt, Katrin Gronau, Anja Klutzny, Michael Hecker
Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis.
Proteomics: 2007, 7(19);3509-26
[PubMed:17726680] [WorldCat.org] [DOI] (P p)

Laurent Jannière, Danielle Canceill, Catherine Suski, Sophie Kanga, Bérengère Dalmais, Roxane Lestini, Anne-Françoise Monnier, Jérôme Chapuis, Alexander Bolotin, Marina Titok, Emmanuelle Le Chatelier, S Dusko Ehrlich
Genetic evidence for a link between glycolysis and DNA replication.
PLoS One: 2007, 2(5);e447
[PubMed:17505547] [WorldCat.org] [DOI] (I e)

Boris Macek, Ivan Mijakovic, Jesper V Olsen, Florian Gnad, Chanchal Kumar, Peter R Jensen, Matthias Mann
The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis.
Mol Cell Proteomics: 2007, 6(4);697-707
[PubMed:17218307] [WorldCat.org] [DOI] (P p)

Alain Lévine, Françoise Vannier, Cédric Absalon, Lauriane Kuhn, Peter Jackson, Elaine Scrivener, Valérie Labas, Joëlle Vinh, Patrick Courtney, Jérôme Garin, Simone J Séror
Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes.
Proteomics: 2006, 6(7);2157-73
[PubMed:16493705] [WorldCat.org] [DOI] (P p)

H Ludwig, G Homuth, M Schmalisch, F M Dyka, M Hecker, J Stülke
Transcription of glycolytic genes and operons in Bacillus subtilis: evidence for the presence of multiple levels of control of the gapA operon.
Mol Microbiol: 2001, 41(2);409-22
[PubMed:11489127] [WorldCat.org] [DOI] (P p)

B Fry, T Zhu, M M Domach, R R Koepsel, C Phalakornkule, M M Ataai
Characterization of growth and acid formation in a Bacillus subtilis pyruvate kinase mutant.
Appl Environ Microbiol: 2000, 66(9);4045-9
[PubMed:10966427] [WorldCat.org] [DOI] (P p)

  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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