Difference between revisions of "Sandbox"

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* '''Description:''' GTP-binding protein involved in initiation of sporulation <br/><br/>
+
* '''Description:''' prephenate dehydratase <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'''
−
|''obg''
+
|''pheA''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|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''' || GTP-binding protein
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|style="background:#ABCDEF;" align="center"| '''Product''' || prephenate dehydratase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || may be required to stimulate activity of the phosphorelay that activates Spo0A
+
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of phenylalanine
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 4.859  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 5.886  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1284 bp, 428 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 855 bp, 285 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||'' [[spo0B]]'', ''[[pheB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[nadR]]'', ''[[pheB]]''
 
|-
 
|-
 
|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:obg_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:pheA_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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===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/spo0B-obg.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pheBA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10337]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10914]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Binds and hydrolyzes GTP and readily exchanges GDP for GTP
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' Era/Obg family
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[Era]], [[Obg]], [[YphC]], [[YsxC]], [[RbgA]], [[YqeH]], [[ThdF]], [[YyaF]], [[YnbA]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 65: Line 63:
  
 
* '''Domains:'''  
 
* '''Domains:'''  
−
Obg possesses 3 domains: A N-terminal glycine-rich domain (1–158), a GTP binding domain (159–342) and a C-terminal TGS domain (343–428). The TGS domain has no known function, but it is named for three protein families in which it is found, ThrRS, GTPase, and SpoT.
 
  
 
* '''Modification:'''
 
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
−
GDP, GTP and probably ppGpp
 
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
 
* '''Interactions:'''
 
* '''Interactions:'''
−
Interaction with Rsb proteins.
 
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 81: Line 76:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''[http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=1LNZ 1LNZ]
+
* '''Structure:'''
 +
 
 +
* '''Swiss prot entry:'''
  
−
* '''Swiss prot entry:'''[http://www.uniprot.org/uniprot/P20964]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU27900]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU27920]
 
 
* '''E.C. number:'''
 
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
−
The biochemical analysis of bacterial and human Obg proteins combined with the structural observation of the ppGpp nucleotide within the Obg active site suggest a potential role for ppGpp modulation of Obg function in ''B. subtilis''.
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[spo0B]]-[[obg]]''
+
* '''Operon:''' ''[[pheB]]-[[pheA]]''
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 119: Line 113:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Naotake Ogasawara]], Nara, Japan
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 126: Line 118:
 
=References=
 
=References=
  
−
# Morimoto T, Loh PC, Hirai T, Asai K, Kobayashi K, Moriya S, Ogasawara N (2002) Six GTP-binding proteins of the Era/Obg family are essential for cell growth in ''Bacillus subtilis''. ''Microbiology'' '''148:''' 3539-3552. [http://www.ncbi.nlm.nih.gov/sites/entrez/12427945 PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Buglino J., Shen V., Hakiman P. & Lima C.D. (2002) Structural and biochemical analysis of the Obg GTP binding protein ''Structure'' '''10:''' 1581-1592. [http://www.ncbi.nlm.nih.gov/pubmed/12429099?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]
 
−
# Scott, J.M., Ju, J., Mitchell, T., and Haldenwang, W.G. (2000) The Bacillus subtilis GTP binding protein obg and regulators of the sigma(B) stress response transcription factor cofractionate with ribosomes ''J. Bacteriol.'' '''182:''' 2771–2777. [http://www.ncbi.nlm.nih.gov/pubmed/10781545?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]
 

Revision as of 18:27, 15 April 2009

  • Description: prephenate dehydratase

Gene name pheA
Synonyms
Essential no
Product prephenate dehydratase
Function biosynthesis of phenylalanine
MW, pI 31 kDa, 5.886
Gene length, protein length 855 bp, 285 aa
Immediate neighbours nadR, pheB
Hier soll was neues rein
Genetic context
PheA 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:

Database entries

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

Additional information

Expression and regulation

  • 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. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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