Difference between revisions of "YmdB"

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(Biological materials)
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===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 
 
* strong overexpression of ''[[hag]]'' {{PubMed|21856853}}
 
* strong overexpression of ''[[hag]]'' {{PubMed|21856853}}
* defective in [[biofilm formation]] {{PubMed|21856853}}
+
* defective in [[biofilm formation]] {{PubMed|21856853,22113911}}
 
* the phenotypes of the ''ymdB'' mutant can be suppressed by overexpression of ''[[slrR]]'' {{PubMed|21856853}}
 
* the phenotypes of the ''ymdB'' mutant can be suppressed by overexpression of ''[[slrR]]'' {{PubMed|21856853}}
  
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=References=
 
=References=
 +
<pubmed> 22113911 </pubmed>
 
  <big>''Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J''  </big>   
 
  <big>''Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J''  </big>   
 
  <big>'''A Novel Factor Controlling Bistability in ''Bacillus subtilis'': The YmdB Protein Affects</big>
 
  <big>'''A Novel Factor Controlling Bistability in ''Bacillus subtilis'': The YmdB Protein Affects</big>
Line 145: Line 145:
 
  J Bacteriol.: 2011, 193(21):5997-6007.  
 
  J Bacteriol.: 2011, 193(21):5997-6007.  
 
  [http://www.ncbi.nlm.nih.gov/pubmed/21856853 PubMed:21856853]
 
  [http://www.ncbi.nlm.nih.gov/pubmed/21856853 PubMed:21856853]
 
  
 
==Functional and structural analysis of orthologs in other organisms==
 
==Functional and structural analysis of orthologs in other organisms==

Revision as of 17:44, 25 November 2011

  • Description: putative phosphatase/ phosphodiesterase, controls bistable gene expression

Gene name ymdB
Synonyms
Essential no
Product putative phosphatase/ phosphodiesterase
Function control of bistable gene expression
MW, pI 29,1 kDa, 6.50
Gene length, protein length 792 bp, 264 amino acids
Immediate neighbours rny, spoVS
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YmdB context.gif
This image was kindly provided by SubtiList



Categories containing this gene/protein

biofilm formation

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag: BSU16970

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: phosphatase activity toward phosphoenolpyruvate and phosphodiesterase activity toward 2',3'-cAMP (the Deinococcus ortholog) PubMed
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:

Database entries

  • Structure: 1T70 (the protein of Deinococcus radiodurans, 44% identity) PubMed
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: constitutive
  • Regulatory mechanism:
  • Additional information: there is a terminator between rny and ymdB, most transcripts terminate there PubMed

Biological materials

  • Mutant:
    • GP583 (spc), available in Stülke lab
    • GP922 (cat), available in Stülke lab
    • GP921 (spc) NCIB3610 derivate, available in Stülke lab
    • GP969 (ymdB(E39Q)-cat) inactive enzyme, available in Stülke lab
  • Expression vector:
    • for expression/ purification from B. subtilis with N-terminal Strep-tag, for SPINE, in pGP380: pGP1041, available in Stülke lab
    • for expression/ purification from B. subtilis with C-terminal Strep-tag, for SPINE, in pGP382: pGP1919, available in Stülke lab
    • for expression/ purification from E. coli with N-terminal His-tag, in pWH844: pGP1040, available in Stülke lab
    • for expression/ purification from E. coli with N-terminal Strep-tag, in pGP172: pGP1917, available in Stülke lab
    • GP970 (ymdB-Strep (cat)), purification from B. subtilis, for SPINE, available in Stülke lab
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab
  • FLAG-tag construct: GP1018 (spc, based on pGP1331), available in the Stülke lab
  • Antibody:

Labs working on this gene/protein

Jörg Stülke, University of Göttingen, Germany Homepage

Your additional remarks

References

Eric R Pozsgai, Kris M Blair, Daniel B Kearns
Modified mariner transposons for random inducible-expression insertions and transcriptional reporter fusion insertions in Bacillus subtilis.
Appl Environ Microbiol: 2012, 78(3);778-85
[PubMed:22113911] [WorldCat.org] [DOI] (I p)

Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J    
A Novel Factor Controlling Bistability in Bacillus subtilis: The YmdB Protein Affects
Flagellin Expression and Biofilm Formation. 
J Bacteriol.: 2011, 193(21):5997-6007. 
PubMed:21856853

Functional and structural analysis of orthologs in other organisms

Jason Zemansky, Benjamin C Kline, Joshua J Woodward, Jess H Leber, Hélène Marquis, Daniel A Portnoy
Development of a mariner-based transposon and identification of Listeria monocytogenes determinants, including the peptidyl-prolyl isomerase PrsA2, that contribute to its hemolytic phenotype.
J Bacteriol: 2009, 191(12);3950-64
[PubMed:19376879] [WorldCat.org] [DOI] (I p)

Dong Hae Shin, Michael Proudfoot, Hyo Jin Lim, In-Kyu Choi, Hisao Yokota, Alexander F Yakunin, Rosalind Kim, Sung-Hou Kim
Structural and enzymatic characterization of DR1281: A calcineurin-like phosphoesterase from Deinococcus radiodurans.
Proteins: 2008, 70(3);1000-9
[PubMed:17847097] [WorldCat.org] [DOI] (I p)