GdpP

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  • Description: cyclic di-AMP phosphodiesterase



Gene name gdpP
Synonyms yybT
Essential no
Product c-di-AMP phosphodiesterase
Function control of sporulation initiation, cell wall homeostasis
Gene expression levels in SubtiExpress: gdpP
MW, pI 74 kDa, 4.865
Gene length, protein length 1977 bp, 659 aa
Immediate neighbours rplI, yybS
Sequences Protein DNA DNA_with_flanks
Genetic context
YybT context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
GdpP expression.png















Categories containing this gene/protein

metabolism of signalling nucleotides

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag: BSU40510

Phenotypes of a mutant

  • inactivation of gdpP strongly restores beta-lactam resistance in a sigM mutant PubMed

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
    • cyclic dinucleotide phosphodiesterase, hydrolysis of di-cyclic AMP PubMed
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
    • N-terminal domain that shares minimum sequence homology with Haem-binding Per-ARNT-Sim (PAS) domains (80 aa) PubMed
    • degenerate GGDEF domain (aa 173 - 301) PubMed
    • DHH/ DHHA1 phosphodiesterase domain PubMed
  • Modification:
  • Cofactor(s): b-type heme with 1:1 stoichiometry PubMed
  • Effectors of protein activity:
    • ppGpp inhibits cyclic dinucleotide phosphodiesterase activity PubMed
    • Heme binding suppresses phosphodiesterase activity PubMed

Database entries

  • Structure:
    • 2M1C (N-terminal PAS domain of GdpP from Geobacillus thermodenitrificans) PubMed
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Sigma factor:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:
    • there is an internal SigD-dependent antisense transcript (as-gdpP) PubMed

Biological materials

  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

Edward Tan, Feng Rao, Swathi Pasunooti, Thi Huong Pham, Ishin Soehano, Mark S Turner, Chong Wai Liew, Julien Lescar, Konstantin Pervushin, Zhao-Xun Liang
Solution structure of the PAS domain of a thermophilic YybT protein homolog reveals a potential ligand-binding site.
J Biol Chem: 2013, 288(17);11949-59
[PubMed:23504327] [WorldCat.org] [DOI] (I p)

Yun Luo, John D Helmann
A σD-dependent antisense transcript modulates expression of the cyclic-di-AMP hydrolase GdpP in Bacillus subtilis.
Microbiology (Reading): 2012, 158(Pt 11);2732-2741
[PubMed:22956758] [WorldCat.org] [DOI] (I p)

Yun Luo, John D Helmann
Analysis of the role of Bacillus subtilis σ(M) in β-lactam resistance reveals an essential role for c-di-AMP in peptidoglycan homeostasis.
Mol Microbiol: 2012, 83(3);623-39
[PubMed:22211522] [WorldCat.org] [DOI] (I p)

Yaara Oppenheimer-Shaanan, Ezequiel Wexselblatt, Jehoshua Katzhendler, Eylon Yavin, Sigal Ben-Yehuda
c-di-AMP reports DNA integrity during sporulation in Bacillus subtilis.
EMBO Rep: 2011, 12(6);594-601
[PubMed:21566650] [WorldCat.org] [DOI] (I p)

Feng Rao, Qiang Ji, Ishin Soehano, Zhao-Xun Liang
Unusual heme-binding PAS domain from YybT family proteins.
J Bacteriol: 2011, 193(7);1543-51
[PubMed:21257773] [WorldCat.org] [DOI] (I p)

Feng Rao, Rui Yin See, Dongwei Zhang, Delon Chengxu Toh, Qiang Ji, Zhao-Xun Liang
YybT is a signaling protein that contains a cyclic dinucleotide phosphodiesterase domain and a GGDEF domain with ATPase activity.
J Biol Chem: 2010, 285(1);473-82
[PubMed:19901023] [WorldCat.org] [DOI] (I p)

GdpP homologs in other organisms

Linda M Holland, Sinéad T O'Donnell, Dmitri A Ryjenkov, Larissa Gomelsky, Shawn R Slater, Paul D Fey, Mark Gomelsky, James P O'Gara
A staphylococcal GGDEF domain protein regulates biofilm formation independently of cyclic dimeric GMP.
J Bacteriol: 2008, 190(15);5178-89
[PubMed:18502872] [WorldCat.org] [DOI] (I p)