Difference between revisions of "Sandbox"

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* '''Description:''' sporulation initiation phosphotransferase <br/><br/>
+
* '''Description:''' GTP-binding protein involved in initiation of sporulation <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'''
−
|''spo0B''
+
|''obg''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spo0D ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || Yes
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || sporulation initiation phosphotransferase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || GTP-binding protein
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || initiation of sporulation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || may be required to stimulate activity of the phosphorelay that activates Spo0A
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 4.963  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 4.859  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 576 bp, 192 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1284 bp, 428 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[obg]]'', ''[[rpmA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||'' [[spo0B]]'', ''[[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:spo0B_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:obg_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 38: Line 38:
  
 
===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/spo0B-obg.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/spo0B-obg.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10336]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10337]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' Binds and hydrolyzes GTP and readily exchanges GDP for GTP
  
−
* '''Protein family:'''
+
* '''Protein family:''' Era/Obg family
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[Era]], [[Obg]], [[YphC]], [[YsxC]], [[RbgA]], [[YqeH]], [[ThdF]], [[YyaF]], [[YnbA]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 63: Line 65:
  
 
* '''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 76: Line 81:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:'''[http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=1LNZ 1LNZ]
−
 
 
−
* '''Swiss prot entry:'''
 
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU27930]
+
* '''Swiss prot entry:'''[http://www.uniprot.org/uniprot/P20964]
  
 +
* '''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=
Line 90: Line 96:
 
* '''Operon:''' ''[[spo0B]]-[[obg]]''
 
* '''Operon:''' ''[[spo0B]]-[[obg]]''
  
−
* '''[[Sigma factor]]:''' [[SigA]]
+
* '''Sigma factor:''' [[SigA]]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 113: Line 119:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Naotake Ogasawara]], Nara, Japan
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 118: Line 126:
 
=References=
 
=References=
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
# 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]
 +
# 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: GTP-binding protein involved in initiation of sporulation

Gene name obg
Synonyms
Essential Yes
Product GTP-binding protein
Function may be required to stimulate activity of the phosphorelay that activates Spo0A
MW, pI 47 kDa, 4.859
Gene length, protein length 1284 bp, 428 aa
Immediate neighbours spo0B, pheB
Hier soll was neues rein
Genetic context
Obg context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

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: Binds and hydrolyzes GTP and readily exchanges GDP for GTP
  • Protein family: Era/Obg family

Extended information on the protein

  • Kinetic information:
  • 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:
  • Cofactor(s):

GDP, GTP and probably ppGpp

  • Effectors of protein activity:
  • Interactions:

Interaction with Rsb proteins.

  • Localization:

Database entries

  • Swiss prot entry:[3]
  • KEGG entry: [4]
  • E.C. number:

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

  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Naotake Ogasawara, Nara, Japan

Your additional remarks

References

  1. 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. PubMed
  2. Buglino J., Shen V., Hakiman P. & Lima C.D. (2002) Structural and biochemical analysis of the Obg GTP binding protein Structure 10: 1581-1592. PubMed
  3. 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. PubMed
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