Difference between revisions of "Sandbox"

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−
* '''Description:''' purine nucleoside phosphorylase <br/><br/>
+
* '''Description:''' phosphoribosylformylglycinamidine synthase <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'''
−
|''punA''
+
|''purL''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''pnp, yqkO ''
+
|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''' || purine nucleoside phosphorylase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoribosylformylglycinamidine synthase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || purine salvage and interconversion
+
|style="background:#ABCDEF;" align="center"|'''Function''' || purine biosynthesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 4.86  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 80 kDa, 4.554  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 813 bp, 271 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2226 bp, 742 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dacF]]'', ''[[drm]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[purQ]]'', ''[[purF]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14281&#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:CAB12468&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:punA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:purL_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:''' BSU23490
+
* '''Locus tag:''' BSU06480
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/drm-punA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/purEKBCSQLFMNHD.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11330]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10705]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate (according to Swiss-Prot) RNA(n+1) + phosphate = RNA(n) + a nucleoside diphosphate (according to Swiss-Prot)  
+
* '''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)  
  
−
* '''Protein family:''' PNP/MTAP phosphorylase family (according to Swiss-Prot) polyribonucleotide nucleotidyltransferase family (according to Swiss-Prot)
+
* '''Protein family:''' FGAMS family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylation on Ser-28 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[PurS]]-[[PurQ]]-[[PurL]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15301530 PubMed]
  
−
* '''Localization:''' secreted (according to Swiss-Prot)
+
* '''Localization:''' cytoplasm (according to Swiss-Prot),  membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 78: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P46354 P46354]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P12042 P12042]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23490]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU06480]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.4.2.1 2.4.2.1]  2.7.7.8]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/6.3.5.3 6.3.5.3]
  
 
=== 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:'''  
+
* '''Operon:''' ''[[purE]]-[[purK]]-[[purB]]-[[purC]]-[[purS]]-[[purQ]]-[[purL]]-[[purF]]-[[purM]]-[[purN]]-[[purH]]-[[purD]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3036807 PubMed]
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/3036807 PubMed]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
 +
** 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]
  
 
* '''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:'''  
+
* '''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]
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>17218307, </pubmed>
+
<pubmed>18763711, </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]
+
# 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]
 +
# 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]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 13:31, 8 June 2009

  • Description: phosphoribosylformylglycinamidine synthase

Gene name purL
Synonyms
Essential no
Product phosphoribosylformylglycinamidine synthase
Function purine biosynthesis
MW, pI 80 kDa, 4.554
Gene length, protein length 2226 bp, 742 aa
Immediate neighbours purQ, purF
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
PurL context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU06480

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: ATP + N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide + L-glutamine + H2O = ADP + phosphate + 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine + L-glutamate (according to Swiss-Prot)
  • Protein family: FGAMS family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization: cytoplasm (according to Swiss-Prot), membrane associated PubMed

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

  • subject to Clp-dependent proteolysis upon glucose starvation PubMed

Expression and regulation

  • Regulation:
    • repressed in the presence of adenine or adenosine(PurR) PubMed
    • repressed in the presence of guanine(G-box) PubMed
  • Additional information: subject to Clp-dependent proteolysis upon glucose starvation PubMed

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

  1. Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 PubMed
  2. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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