Difference between revisions of "Sandbox"

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* '''Description:''' transcriptional regulator of transition state genes <br/><br/>
+
* '''Description:''' write here <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'''
−
|''abrB''
+
|''aadK''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cpsX ''
+
|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''' || transcriptional regulator
+
|style="background:#ABCDEF;" align="center"| '''Product''' || aminoglycoside 6-adenylyltransferase (EC 2.7.7.-)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of gene expression during the transition from growth to stationary phase
+
|style="background:#ABCDEF;" align="center"|'''Function''' ||  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 10 kDa, 6.57  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.755  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 288 bp, 96 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 852 bp, 284 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yabC]]'', ''[[metS]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yrdA]]'', ''[[yrpB]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/abrB_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/aadK_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/abrB_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/aadK_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:abrB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:aadK_context.gif]]
 
|-
 
|-
 
|}
 
|}
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===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
No swarming motility on B medium. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/abrB.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10100]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11037]
  
 
=== Additional information===
 
=== Additional information===
Line 58: Line 56:
 
* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[Abh]], [[SpoVT]] (only N-terminal domain)
+
* '''Paralogous protein(s):'''
−
 
 
−
=== Genes/ operons controlled by AbrB ===
 
−
 
 
−
* '''Activated by AbrB:''' ''[[citB]]'', ''[[comK]], [[hpr]]'', ''[[rbsR]]-[[rbsK]]-[[rbsD]]-[[rbsA]]-[[rbsC]]-[[rbsB]]''
 
−
 
 
−
* ''' Repressed by AbrB:''' ''[[abrB]], [[aprE]], [[ftsA]]-[[ftsZ]], [[kinC]], [[motA]], [[nprE]], [[pbpE]], [[spo0H]], [[spoVG]], [[spo0E]], [[tycA]], [[sbo]]-[[alb]], [[yqxM]]-[[sipW]]-[[tasA]]''
 
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 76: Line 68:
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:''' interaction with [[AbbA]] results in inactivation of AbrB [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
+
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[AbrB]]-[[AbbA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
+
* '''Interactions:'''
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 84: Line 76:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' 1Z0R (N-terminal DNA recognition domain)  [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=32611 NCBI] [http://www.ncbi.nlm.nih.gov/sites/entrez/16223496 PubMed]
+
* '''Structure:'''
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:'''
+
* '''KEGG entry:''' http://www.genome.jp/dbget-bin/www_bget?bsu+BSU26790
 +
 
 +
 
 +
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''abrB'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
+
* '''Sigma factor:'''  
  
−
* '''Regulation:''' expressed at the onset of stationary phase [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' repressed by [[Spo0A]]-P [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' TT731 (aphA3)
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 120: Line 114:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]
 
−
 
−
[[Mark Strauch]], Baltimore, USA [http://lifesciences.umaryland.edu/Pages/faculty_profile.aspx?ID=212 homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 129: Line 119:
 
=References=
 
=References=
  
−
# Banse et al. (2008) Parallel pathways of repression and antirepression governing the transition to stationary phase in ''Bacillus subtilis''.''Proc. Natl. Acad. Sci. USA'' '''105:''' 15547-15552. [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
 
−
# Perego et al. (1988) Structure of the gene for the transition state regulator, ''abrB'': regulator synthesis is controlled by the ''spo0A'' sporulation gene in ''Bacillus subtilis''. ''Mol. Microbiol.'' '''2:''' 689-699. [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
 
−
# Xu, K. and M.A. Strauch. (1996) In vitro selection of optimal AbrB-binding sites: comparison to known in vivo sites indicates flexibility in AbrB-binding and recognition of three-dimensional DNA structures. Molec. Microbiol. 19: 145-158 [http://www.ncbi.nlm.nih.gov/sites/entrez/8821944 PubMed]
 
−
# Xu, K., D. Clark and M.A. Strauch. (1996) Analysis of abrB mutations, mutant proteins, and why abrB does not utilize a perfect consensus in the –35 region of its sigmaA promoter.J. Biol. Chem. 271:2621-2626 [http://www.ncbi.nlm.nih.gov/sites/entrez/8576231 PubMed]
 
−
# Vaughn, J.L., Feher V., Naylor, S., Strauch, M.A. and J. Cavanagh. (2000) Novel DNA binding domain and genetic regulation model of Bacillus subtilis transition state regulator AbrB. Nature Structural Biology 7:1139-1146; [http://www.ncbi.nlm.nih.gov/sites/entrez/11101897 PubMed], Corrigendum appears in Nature Stuctural & Molecular Biology (2005) 12:380
 
−
# Xu, K. and M.A. Strauch. (2001) DNA-binding activity of amino-terminal domains of the Bacillus subtilis AbrB protein. J. Bacteriol. 183:4094-4098 [http://www.ncbi.nlm.nih.gov/sites/entrez/11395475 PubMed]
 
−
# Phillips, Z. E.V. and M.A. Strauch. (2001) Role of Cys54 in AbrB multimerization and DNA-binding activity. FEMS Microbiol. Letters. 203:207-210 [http://www.ncbi.nlm.nih.gov/sites/entrez/11583849 PubMed]
 
−
# Phillips, Z.E.V. and M.A. Strauch. (2002) Bacillus subtilis sporulation and stationary phase gene expression. Cellular and Molecular Life Sciences 59:392-402 [http://www.ncbi.nlm.nih.gov/sites/entrez/11964117 PubMed]
 
−
# Shafikhani, S.H., Mandic-Mulec, I., Strauch, M.A., Smith, I. and T. Leighton. (2002) Postexponential regulation of sin operon expression in Bacillus subtilis. J. Bacteriol. 184:564-571 [http://www.ncbi.nlm.nih.gov/sites/entrez/11751836 PubMed]
 
−
# Benson, L. M., Vaughn, J. L., Strauch, M. A., Bobay, B. G., Thompson, R., Naylor, S. and J. Cavanagh (2002). Macromolecular assembly of the transition state regulator AbrB in its unbound and complexed states probed by microelectrospray ionization mass spectrometry. Analytical Biochemistry 306:222-227 [http://www.ncbi.nlm.nih.gov/sites/entrez/12123659 PubMed]
 
−
# Qian, Q., Lee, C.Y., Helmann, J. and M.A. Strauch. (2002) AbrB regulation of the sigmaW regulon of Bacillus subtilis. FEMS Microbiol. Letters 211:219-223. [http://www.ncbi.nlm.nih.gov/sites/entrez/12076816 PubMed]
 
−
# Kim, H. J., S. I. Kim, M. Ratnayake-Lecamwasam, K. Tachikawa, A. L. Sonenshein, and M. Strauch. (2003) Complex regulation of the Bacillus subtilis aconitase gene. J. Bacteriol. 185:1672-1680. [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed]
 
−
# Bobay, B.G., Benson, L., Naylor, S., Feeney, B., Clark, A.C., Goshe, M.B., Strauch, M.A., Thompson, R., and J.Cavanagh. (2004) Evaluation of the DNA binding tendencies of the transition state regulator AbrB. Biochemistry. 43:16106-16118. [http://www.ncbi.nlm.nih.gov/sites/entrez/15610005 PubMed]
 
−
# Bobay et al.(2005) Revised structure of the AbrB N-terminal domain unifies a diverse superfamily of putative DNA-binding proteins. FEBS Lett. 579:5669-5674. [http://www.ncbi.nlm.nih.gov/sites/entrez/16223496 PubMed]
 
−
# Yao, F and M.A. Strauch (2005) Independent and Interchangeable Multimerization Domains of the AbrB, Abh and SpoVT Global Regulatory Proteins. J. Bacteriol. 187:6354-6362 [http://www.ncbi.nlm.nih.gov/sites/entrez/16159768 PubMed]
 
−
# Bobay, B.G., Mueller, G.A., Thompson, R.J., Venters, R.A., Murzin, A.G., Strauch, M.A. & J. Cavanagh (2006) NMR structure of AbhN and comparison with AbrBN: First Insights into the DNA-binding Promiscuity and Specificity of AbrB-like Transition-state Regulator Proteins. J. Biol. Chem. 281:21399-21409  [http://www.ncbi.nlm.nih.gov/sites/entrez/16702211 PubMed]
 
−
# Jordan S. Rietkötter E. Strauch MA. Kalamorz F. Butcher BG. Helmann JD. Mascher T. (2007) LiaRS-dependent gene expression is embedded in transition state regulation in Bacillus subtilis. Microbiology. 153: 2530-2540. [http://www.ncbi.nlm.nih.gov/sites/entrez/17660417 PubMed]
 
−
# Strauch MA. Bobay BG. Cavanagh J. Yao F. Wilson A. Le Breton Y. (2007) Abh and AbrB control of Bacillus subtilis antimicrobial gene expression. J. of Bacteriol. 189:7720-7732. [http://www.ncbi.nlm.nih.gov/sites/entrez/17720793 PubMed]
 
−
# Hamze et al. (2009) Identification of genes required for different stages of dendritic swarming in ''Bacillus subtilis'', with a novel role for ''phrC''.  ''Microbiology'' '''155:''' 398-412. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]
 
−
# Strauch MA. (1995) AbrB modulates expression and catabolite repression of a Bacillus subtilis ribose transport operon. ''J Bacteriol.'' '''Dec;177(23):'''6727-31. [http://www.ncbi.nlm.nih.gov/sites/entrez/7592460 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 14:38, 19 March 2009

  • Description: write here

Gene name aadK
Synonyms
Essential no
Product aminoglycoside 6-adenylyltransferase (EC 2.7.7.-)
Function
MW, pI 33 kDa, 4.755
Gene length, protein length 852 bp, 284 aa
Immediate neighbours yrdA, yrpB
Gene sequence (+200bp) Protein sequence
Genetic context
AadK context.gif



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

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:


  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • 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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