Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' RNase Y, endoribonuclease, required for the processing of the ''[[gapA]]'' operon mRNA<br/><br/>
+
* '''Description:''' penicillin-binding protein X <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'''
−
|''rny''
+
|''pbpX''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ymdA''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || RNase Y
+
|style="background:#ABCDEF;" align="center"| '''Product''' || penicillin-binding protein X
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || required for the processing <br/>of the ''[[gapA]]'' operon mRNA
+
|style="background:#ABCDEF;" align="center"|'''Function''' || endopeptidase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 58,7 kDa, 5.39
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 9.711 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1560 bp, 520 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1173 bp, 391 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pbpX]]'', ''[[ymdB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[recA]]'', ''[[rny]]''
 
|-
 
|-
 
|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:pbpX_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:rny_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 31: Line 29:
 
__TOC__
 
__TOC__
  
−
<br/><br/><br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
Line 37: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 1766580 - 1768139
+
* '''Coordinates:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pbpX.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13420]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12642]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 55: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' required for the processing of the ''[[gapA]]'' operon mRNA  [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' 2',3' cyclic nucleotide phosphodiesterase family
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 66: Line 63:
  
 
* '''Domains:'''  
 
* '''Domains:'''  
−
** transmembrane domain (4–24)
 
−
** KH domain (210–273)
 
−
** HD domain (336–429)
 
  
 
* '''Modification:'''
 
* '''Modification:'''
  
−
* '''Cofactor(s):''' metal-dependent
+
* '''Cofactor(s):'''
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[Rny]]-[[PfkA]], [[Rny]]-[[Eno]], [[Rny]]-[[PnpA]], [[Rny]]-[[RnjA]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
+
* '''Interactions:'''
  
−
* '''Localization:''' Single-pass membrane protein [http://www.ncbi.nlm.nih.gov/sites/entrez/17005971 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
* '''Localization:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed],  localizes during sporulation to both asymmetric septa and the prespore [http://www.ncbi.nlm.nih.gov/sites/entrez/15758244 Link to a summary]
  
 
=== Database entries ===
 
=== Database entries ===
Line 84: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31774]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16960]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16950]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.4.16 3.1.4.16]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
  
−
required for the processing of the ''[[gapA]]'' operon mRNA
 
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[rny]]-[[ymdB]]''
+
* '''Operon:'''  
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:''' [[SigX]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15758244 Link to a summary]
  
−
* '''Regulation:''' constitutive
+
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:''' there is a terminator between ''rny'' and ''[[ymdB]]'', most transcripts terminate there
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' essential!!!!, 4043 (''rny'' under p-spac control), GP193 (''rny'' under p-xyl control), available in [[Stülke]] lab
+
* '''Mutant:'''
−
 
 
−
* '''Expression vector:'''
 
−
 
 
−
N-terminal Strep-tag, expression in ''E. coli'', in [[pGP172]]: pGP441, available in [[Stülke]] lab
 
  
−
N-terminal Strep-tag, for SPINE, expression in ''B. subtilis'', in [[pGP380]]: pGP775 , available in [[Stülke]] lab
+
* '''Expression vector:'''
 +
       
 +
* '''lacZ fusion:'''
  
−
wild type ''rny'', expression in B. subtilis, in [[pBQ200]]: pGP1201, available in [[Stülke]] lab
+
* '''GFP fusion:'''
  
−
there is also a series of domain constructs present in [[pBQ200]], all available in [[Stülke]] lab
+
* '''two-hybrid system:'''  
−
 
−
* '''lacZ fusion:''' pGP459 (in [[pAC7]]), available in [[Stülke]] lab
 
  
−
* '''GFP fusion:''' B. subtilis 3569 (amyE:: (p-xyl rny-gfpmut1-spc)), available in [[Errington]] lab
+
* '''Antibody:'''
−
 
 
−
* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
 
−
 
 
−
* '''Antibody:''' available in [[van Dijl]] and [[Stülke]] labs
 
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Harald Putzer]], IBPC Paris, France [http://www.ibpc.fr/UPR9073/putzer/recherches_harald.htm Homepage]
 
−
 
−
[[Stülke|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 137: Line 118:
 
=References=
 
=References=
  
−
# 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]
+
# Voigt et al. (2009) Cell physiology and protein secretion of ''Bacillus licheniformis'' compared to ''Bacillus subtilis''. ''J Mol Microbiol Biotechnol.'' '''16:''' 53-68 [http://www.ncbi.nlm.nih.gov/pubmed/18957862 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]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Hunt, A., Rawlins, J. P., Thomaides, H. B., and Errington, J. (2006) Functional analysis of 11 putative essential genes in Bacillus subtilis. Microbiology 152, 2895-2907. [http://www.ncbi.nlm.nih.gov/sites/entrez/17005971 PubMed]
 

Revision as of 19:45, 15 April 2009

  • Description: penicillin-binding protein X

Gene name pbpX
Synonyms
Essential no
Product penicillin-binding protein X
Function endopeptidase
MW, pI 43 kDa, 9.711
Gene length, protein length 1173 bp, 391 aa
Immediate neighbours recA, rny
Hier soll was neues rein
Genetic context
PbpX context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: extracellular (signal peptide) PubMed, localizes during sporulation to both asymmetric septa and the prespore Link to a summary

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:

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

  1. Voigt et al. (2009) Cell physiology and protein secretion of Bacillus licheniformis compared to Bacillus subtilis. J Mol Microbiol Biotechnol. 16: 53-68 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=55942"