Difference between revisions of "YmdB"

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(Database entries)
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
* '''Catalyzed reaction/ biological activity:''' phosphatase activity toward phosphoenolpyruvate and phosphodiesterase activity toward 2',3'-cAMP (the ''Deinococcus'' ortholog) {{PubMed|17847097}}
+
* '''Catalyzed reaction/ biological activity:'''  
 +
** phosphodiesterase activity toward 2',3'-cAMP {{PubMed|24163345}}
  
 
* '''Protein family:'''
 
* '''Protein family:'''
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=== Database entries ===
 
=== Database entries ===
  
* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=4B2O 4B2O]
+
* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=4B2O 4B2O] {{PubMed|24163345}}
  
 
* '''UniProt:''' [http://www.uniprot.org/uniprot/O31775 O31775]
 
* '''UniProt:''' [http://www.uniprot.org/uniprot/O31775 O31775]
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=References=
 
=References=
<pubmed>21856853 22211522,22113911</pubmed>
+
<pubmed>21856853 22211522,22113911 24163345 </pubmed>
 
==Functional and structural analysis of orthologs in other organisms==
 
==Functional and structural analysis of orthologs in other organisms==
 
<pubmed> 19376879 17847097 </pubmed>
 
<pubmed> 19376879 17847097 </pubmed>
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 12:28, 29 October 2013

  • 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

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:
  • Domains:
  • Modification:
  • Cofactor(s):
  • 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

  • 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

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)