YmdB

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  • Description: phosphodiesterase, controls bistable gene expression

Gene name ymdB
Synonyms
Essential no
Product phosphodiesterase
Function control of bistable gene expression
Gene expression levels in SubtiExpress: ymdB
MW, pI 29,1 kDa, 6.50
Gene length, protein length 792 bp, 264 amino acids
Immediate neighbours rny, spoVS
Sequences Protein DNA DNA_with_flanks
Genetic context
YmdB context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
YmdB expression.png















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

  • strong overexpression of hag PubMed
  • defective in biofilm formation PubMed
  • the phenotypes of the ymdB mutant can be suppressed by overexpression of slrR PubMed
  • inactivation of ymdB restores beta-lactam resistance in a sigM mutant PubMed
  • increased expression of genes encoding small acid-soluble proteins PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
    • phosphodiesterase activity toward 2',3'-cAMP PubMed
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Modification:
  • Effectors of protein activity:

Database entries

  • 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

  • Expression vector:
    • for expression/ purification from B. subtilis with N-terminal Strep-tag, for SPINE, in pGP380: pGP1041, available in Jörg Stülke's lab
    • for expression/ purification from B. subtilis with C-terminal Strep-tag, for SPINE, in pGP382: pGP1919, available in Jörg Stülke's lab
    • for expression/ purification from E. coli with N-terminal His-tag, in pWH844: pGP1040, available in Jörg Stülke's lab
    • for expression/ purification from E. coli with N-terminal Strep-tag, in pGP172: pGP1917, available in Jörg Stülke's lab PubMed
    • GP970 (ymdB-Strep (cat)), purification from B. subtilis, for SPINE, available in Jörg Stülke's lab
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Jörg Stülke's lab
  • Antibody:

Labs working on this gene/protein

Jörg Stülke, University of Göttingen, Germany Homepage

Your additional remarks

References

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)