Difference between revisions of "Sandbox"

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−
* '''Description:''' pyruvate kinase, glycolytic enzyme <br/><br/>
+
* '''Description:''' carbamoyl-phosphate synthetase (catalytic subunit) <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''
+
|''pyrAB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''pykA''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|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''' || carbamoyl-phosphate synthetase (catalytic subunit)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || pyrimidine biosynthesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61,9 kDa, 4.88
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 117 kDa, 4.785 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1755 bp, 585 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 3213 bp, 1071 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pfkA]]'', ''[[ytzA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pyrAA]]'', ''[[pyrK]]''
 
|-
 
|-
−
|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" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13426&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:pyk_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:pyrAB_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>
 
|-
 
|-
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU29180
+
* '''Locus tag:''' BSU15520
  
 
===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:''' [http://dbtbs.hgc.jp/COG/prom/pyrRPBCAAABKDFE.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12661]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10716]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 53: Line 52:
 
=== 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:''' 2 ATP + L-glutamine + HCO<sub>3</sub><sup>-</sup> + H<sub>2</sub>O = 2 ADP + phosphate + L-glutamate + carbamoyl phosphate (according to Swiss-Prot)
  
−
* '''Protein family:''' PEP-utilizing enzyme family (according to Swiss-Prot) pyruvate kinase family, (C-terminal section: PEP-utilizing enzyme family)
+
* '''Protein family:''' carB family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[CarB]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 65: Line 64:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''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]
+
* '''Modification:'''
  
−
* '''Cofactor(s):''' magnesium ion, potassium
+
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:''' activated by PEP [http://www.ncbi.nlm.nih.gov/sites/entrez/4623707 PubMed]
+
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''  
+
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
+
* '''Localization:''' membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]  
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''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]
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80885]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P25994 P25994]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29180]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU15520]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.40 2.7.1.40]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/6.3.5.5 6.3.5.5]
  
 
=== 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 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]]''
+
* '''Expression vector:'''
 +
       
 +
* '''lacZ fusion:'''
  
 
* '''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 129: Line 118:
 
=References=
 
=References=
  
−
<pubmed>17726680 16493705 11489127 17505547 10966427 17218307, </pubmed>
+
<pubmed>18763711, </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]
+
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 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: carbamoyl-phosphate synthetase (catalytic subunit)

Gene name pyrAB
Synonyms
Essential no
Product carbamoyl-phosphate synthetase (catalytic subunit)
Function pyrimidine biosynthesis
MW, pI 117 kDa, 4.785
Gene length, protein length 3213 bp, 1071 aa
Immediate neighbours pyrAA, pyrK
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
PyrAB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU15520

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: 2 ATP + L-glutamine + HCO3- + H2O = 2 ADP + phosphate + L-glutamate + carbamoyl phosphate (according to Swiss-Prot)
  • Protein family: carB family (according to Swiss-Prot)
  • Paralogous protein(s): CarB

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: membrane PubMed

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Operon:
  • 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

Hannes Hahne, Susanne Wolff, Michael Hecker, Dörte Becher
From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches.
Proteomics: 2008, 8(19);4123-36
[PubMed:18763711] [WorldCat.org] [DOI] (I p)

  1. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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