Difference between revisions of "Sandbox"

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−
* '''Description:''' unknown <br/><br/>
+
* '''Description:''' phosphofructokinase, 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'''
−
|''ytzA''
+
|''pfkA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''pfk''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || 6-phosphofructokinase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 13 kDa, 10.108 
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34,1 kDa, 6.14
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 381 bp, 127 aa
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 957 bp, 319 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytvI]]'', ''[[pyk]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[accA]]'', ''[[pyk]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14877&#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:CAB14879&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ytzA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:pfkA_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:'''
+
* '''Coordinates:''' 2985630 - 2986586
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential  [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 43: 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+BG13935]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12644]
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=The protein=
 
=The protein=
Line 52: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6-bisphosphate
  
−
* '''Protein family:'''
+
* '''Protein family:''' phosphofructokinase family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
 +
** 3 x nucleotide binding domain (ATP) (21–25), (154–158), (171–187)
  
 
* '''Modification:'''
 
* '''Modification:'''
  
−
* '''Cofactor(s):'''
+
* '''Cofactor(s):''' ATP
  
−
* '''Effectors of protein activity:'''
+
* '''Effectors of protein activity:''' inhibited by citrate, ATP, PEP, Ca2+, and others (in ''B. licheniformes'') [http://www.ncbi.nlm.nih.gov/pubmed/4269800 PubMed]
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[PfkA]]-[[Pgm]], [[PfkA]]-[[Eno]], [[PfkA]]-[[Rny]], [[PfkA]]-[[PnpA]], [[PfkA]]-[[RnjA]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot),  Membrane (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
+
* '''Localization:''' cytoplasm (according to Swiss-Prot),  Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''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]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32064 O32064]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34529 O34529] [http://www.uniprot.org/uniprot/O34529]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29170]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29190]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.11 2.7.1.11]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''pfkA [[pyk]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
  
−
* '''[[[[Sigma factor]]]]:'''  
+
* '''Sigma factor:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' twofold induced by glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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* '''Mutant:'''
 
* '''Mutant:'''
  
−
* '''Expression vector:'''
+
* '''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
−
       
+
−
* '''lacZ fusion:'''
+
* '''lacZ fusion:''' pGP511 (in [[pAC6]]), available in [[Stülke]] lab
  
 
* '''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 119: Line 124:
  
 
# 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]
 
# 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]
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID 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]
 +
# 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]

Revision as of 23:13, 1 May 2009

  • Description: phosphofructokinase, glycolytic enzyme

Gene name pfkA
Synonyms pfk
Essential yes
Product 6-phosphofructokinase
Function catabolic enzyme in glycolysis
MW, pI 34,1 kDa, 6.14
Gene length, protein length 957 bp, 319 amino acids
Immediate neighbours accA, pyk
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
PfkA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates: 2985630 - 2986586

Phenotypes of a mutant

essential PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6-bisphosphate
  • Protein family: phosphofructokinase family
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
    • 3 x nucleotide binding domain (ATP) (21–25), (154–158), (171–187)
  • Modification:
  • Cofactor(s): ATP
  • Effectors of protein activity: inhibited by citrate, ATP, PEP, Ca2+, and others (in B. licheniformes) PubMed
  • Localization: cytoplasm (according to Swiss-Prot), Cytoplasm (Homogeneous) PubMed

Database entries

  • Structure: Geobacillus stearothermophilus NCBI, Mutant form, complex with fructose-6-phosphate Geobacillus stearothermophilus NCBI
  • KEGG entry: [4]

Additional information

Expression and regulation

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

Biological materials

  • Mutant:
  • 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
  • lacZ fusion: pGP511 (in pAC6), available in Stülke lab
  • 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. 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. PubMed
  2. 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 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
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