Difference between revisions of "YmdB"

From SubtiWiki
Jump to: navigation, search
(References)
(Basic information/ Evolution)
Line 57: Line 57:
 
* '''Protein family:'''
 
* '''Protein family:'''
  
* '''Paralogous protein(s):''' similar to unknown proteins
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===

Revision as of 14:22, 6 September 2010

  • Description: putative phosphatase/ phosphodiesterase

Gene name ymdB
Synonyms
Essential no
Product putative phosphatase/ phosphodiesterase
Function unknown function
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



The gene

Basic information

  • Locus tag: BSU16970

Phenotypes of a mutant

strong overexpression of Hag

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:
  • Interactions:
  • Localization:

Database entries

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

Additional information

has a negative effect on hag expression

Expression and regulation

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

Biological materials

  • Mutant:
    • GP583 (spc), available in Stülke lab
    • GP922 (cat), available in Stülke lab
    • GP921 (spc) NCIB3610 derivate, 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 E. coli with N-terminal His-tag, in pWH844: pGP1040, 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)