Difference between revisions of "Sandbox"

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−
* '''Description:''' glycerol-3-phosphate dehydrogenase (menaquinone 7) <br/><br/>
+
* '''Description:''' transcriptional antiterminator of the ''[[glpT]]-[[glpQ]]'' and ''[[glpF]]-[[glpK]]-[[glpD]]'' operons <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'''
−
|''glpD''
+
|''glpP''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
Line 10: Line 10:
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || glycerol-3-phosphate dehydrogenase (menaquinone 7)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional antiterminator
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' ||  
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of glycerol and glycerol-3-phosphate utilization
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62 kDa, 8.002  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 8.104  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1665 bp, 555 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 576 bp, 192 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glpK]]'', ''[[pgcA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhxA]]'', ''[[glpF]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12758&#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:CAB12755&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:glpP_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:glpD_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:''' BSU09300
+
* '''Locus tag:''' BSU09270
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/glpD.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yhxA-glpP.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10188]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10185]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' sn-glycerol 3-phosphate + a quinone = glycerone phosphate + a quinol (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' FAD-dependent glycerol-3-phosphate dehydrogenase family (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 68: Line 66:
 
* '''Modification:'''
 
* '''Modification:'''
  
−
* '''Cofactor(s):''' FAD
+
* '''Cofactor(s):'''
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasm (according to Swiss-Prot)
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P18158 P18158]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P30300 P30300]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU09300]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU09270]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.5.3 1.1.5.3]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[glpD]]''
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' repressed by glucose ([[CcpA]]) 
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 115: Line 113:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Josef Deutscher]], Paris-Grignon, France
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 120: Line 120:
 
=References=
 
=References=
  
−
<pubmed>8825777 1479885 9595668 9493382, </pubmed>
+
<pubmed>8825777 11929549 8436953 9595668 9493382 1479885 1809833 182672, </pubmed>
−
 
 
 
# Glatz E, Nilsson RP, Rutberg L, Rutberg B (1996) A dual role of the ''Bacillus subtilis glpD'' leader and the GlpP protein in the regulated expression of glpD: antitermination and control of mRNA stability. Mol Microbiol 19:319-328. [http://www.ncbi.nlm.nih.gov/sites/entrez/8825777 PubMed]
 
# Glatz E, Nilsson RP, Rutberg L, Rutberg B (1996) A dual role of the ''Bacillus subtilis glpD'' leader and the GlpP protein in the regulated expression of glpD: antitermination and control of mRNA stability. Mol Microbiol 19:319-328. [http://www.ncbi.nlm.nih.gov/sites/entrez/8825777 PubMed]
−
# Holmberg C, Rutberg L (1992) An inverted repeat preceding the ''Bacillus subtilis glpD'' gene is a conditional terminator of transcription. Mol Microbiol 6:2931-2938. [http://www.ncbi.nlm.nih.gov/sites/entrez/1479885 PubMed]
+
# Darbon E, Servant P, Poncet S, Deutscher J (2002) Antitermination by GlpP, catabolite repression via CcpA and inducer exclusion triggered by P~GlpK dephosphorylation control ''Bacillus subtilis glpFK'' expression. Mol Microbiol 43:1039-1052. [http://www.ncbi.nlm.nih.gov/sites/entrez/11929549 PubMed]
 +
# Beijer L, Nilsson RP, Holmberg C, Rutberg L: The ''glpP'' and ''glpF'' genes of the glycerol regulon in ''Bacillus subtilis''. J Gen Microbiol 1993;139:349-359. [http://www.ncbi.nlm.nih.gov/sites/entrez/8436953 PubMed]
 
# Glatz E, Farewell A, Rutberg B: The ''Bacillus subtilis glpD'' leader and antiterminator protein GlpP provide a target for glucose repression in ''Escherichia coli''. FEMS Microbiol Lett 1998;162:93-96. [http://www.ncbi.nlm.nih.gov/sites/entrez/9595668 PubMed]
 
# Glatz E, Farewell A, Rutberg B: The ''Bacillus subtilis glpD'' leader and antiterminator protein GlpP provide a target for glucose repression in ''Escherichia coli''. FEMS Microbiol Lett 1998;162:93-96. [http://www.ncbi.nlm.nih.gov/sites/entrez/9595668 PubMed]
 
# Glatz E, Persson M, Rutberg B: Antiterminator protein GlpP of ''Bacillus subtilis'' binds to ''glpD'' leader mRNA. Microbiology 1998;144:449-456. [http://www.ncbi.nlm.nih.gov/sites/entrez/9493382 PubMed]
 
# Glatz E, Persson M, Rutberg B: Antiterminator protein GlpP of ''Bacillus subtilis'' binds to ''glpD'' leader mRNA. Microbiology 1998;144:449-456. [http://www.ncbi.nlm.nih.gov/sites/entrez/9493382 PubMed]
 +
# Holmberg C, Rutberg L.(1992) An inverted repeat preceding the Bacillus subtilis glpD gene is a conditional terminator of transcription. ''Mol Microbiol.'' '''Oct;6(20):''' 2931-8. [http://www.ncbi.nlm.nih.gov/sites/entrez/1479885 PubMed]
 +
# Holmberg C, Rutberg B. (1991) Expression of the gene encoding glycerol-3-phosphate dehydrogenase (glpD) in Bacillus subtilis is controlled by antitermination. ''Mol Microbiol.'' '''Dec;5(12):''' 2891-900. [http://www.ncbi.nlm.nih.gov/sites/entrez/1809833 PubMed]
 +
# Lindgren V, Rutberg L. (1976) Genetic control of the glp system in Bacillus subtilis. '' J Bacteriol.'' '''Sep;127(3):''' 1047-57. [http://www.ncbi.nlm.nih.gov/sites/entrez/182672 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 14:04, 8 June 2009

Gene name glpP
Synonyms
Essential no
Product transcriptional antiterminator
Function regulation of glycerol and glycerol-3-phosphate utilization
MW, pI 21 kDa, 8.104
Gene length, protein length 576 bp, 192 aa
Immediate neighbours yhxA, glpF
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
GlpP context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU09270

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:

Database entries

  • Structure:
  • 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

Josef Deutscher, Paris-Grignon, France

Your additional remarks

References

Emmanuelle Darbon, Pascale Servant, Sandrine Poncet, Josef Deutscher
Antitermination by GlpP, catabolite repression via CcpA and inducer exclusion triggered by P-GlpK dephosphorylation control Bacillus subtilis glpFK expression.
Mol Microbiol: 2002, 43(4);1039-52
[PubMed:11929549] [WorldCat.org] [DOI] (P p)

E Glatz, A Farewell, B Rutberg
The Bacillus subtilis glpD leader and antiterminator protein GlpP provide a target for glucose repression in Escherichia coli.
FEMS Microbiol Lett: 1998, 162(1);93-6
[PubMed:9595668] [WorldCat.org] [DOI] (P p)

Elisabeth Glatz, Martin Persson, Blanka Rutberg
Antiterminator protein GlpP of Bacillus subtilis binds to glpD leader mRNA.
Microbiology (Reading): 1998, 144 ( Pt 2);449-456
[PubMed:9493382] [WorldCat.org] [DOI] (P p)

E Glatz, R P Nilsson, L Rutberg, B Rutberg
A dual role for the Bacillus subtilis glpD leader and the GlpP protein in the regulated expression of glpD: antitermination and control of mRNA stability.
Mol Microbiol: 1996, 19(2);319-28
[PubMed:8825777] [WorldCat.org] [DOI] (P p)

L Beijer, R P Nilsson, C Holmberg, L Rutberg
The glpP and glpF genes of the glycerol regulon in Bacillus subtilis.
J Gen Microbiol: 1993, 139(2);349-59
[PubMed:8436953] [WorldCat.org] [DOI] (P p)

C Holmberg, L Rutberg
An inverted repeat preceding the Bacillus subtilis glpD gene is a conditional terminator of transcription.
Mol Microbiol: 1992, 6(20);2931-8
[PubMed:1479885] [WorldCat.org] [DOI] (P p)

C Holmberg, B Rutberg
Expression of the gene encoding glycerol-3-phosphate dehydrogenase (glpD) in Bacillus subtilis is controlled by antitermination.
Mol Microbiol: 1991, 5(12);2891-900
[PubMed:1809833] [WorldCat.org] [DOI] (P p)

V Lindgren, L Rutberg
Genetic control of the glp system in Bacillus subtilis.
J Bacteriol: 1976, 127(3);1047-57
[PubMed:182672] [WorldCat.org] [DOI] (P p)

  1. Glatz E, Nilsson RP, Rutberg L, Rutberg B (1996) A dual role of the Bacillus subtilis glpD leader and the GlpP protein in the regulated expression of glpD: antitermination and control of mRNA stability. Mol Microbiol 19:319-328. PubMed
  2. Darbon E, Servant P, Poncet S, Deutscher J (2002) Antitermination by GlpP, catabolite repression via CcpA and inducer exclusion triggered by P~GlpK dephosphorylation control Bacillus subtilis glpFK expression. Mol Microbiol 43:1039-1052. PubMed
  3. Beijer L, Nilsson RP, Holmberg C, Rutberg L: The glpP and glpF genes of the glycerol regulon in Bacillus subtilis. J Gen Microbiol 1993;139:349-359. PubMed
  4. Glatz E, Farewell A, Rutberg B: The Bacillus subtilis glpD leader and antiterminator protein GlpP provide a target for glucose repression in Escherichia coli. FEMS Microbiol Lett 1998;162:93-96. PubMed
  5. Glatz E, Persson M, Rutberg B: Antiterminator protein GlpP of Bacillus subtilis binds to glpD leader mRNA. Microbiology 1998;144:449-456. PubMed
  6. Holmberg C, Rutberg L.(1992) An inverted repeat preceding the Bacillus subtilis glpD gene is a conditional terminator of transcription. Mol Microbiol. Oct;6(20): 2931-8. PubMed
  7. Holmberg C, Rutberg B. (1991) Expression of the gene encoding glycerol-3-phosphate dehydrogenase (glpD) in Bacillus subtilis is controlled by antitermination. Mol Microbiol. Dec;5(12): 2891-900. PubMed
  8. Lindgren V, Rutberg L. (1976) Genetic control of the glp system in Bacillus subtilis. J Bacteriol. Sep;127(3): 1047-57. PubMed
  9. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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