GdpP

• 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
Get the DNA and protein sequences (Barbe et al., 2009)
Genetic context This image was kindly provided by SubtiList
Expression at a glance   PubMed

Categories containing this gene/protein

metabolism of signalling nucleotides

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]

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

• Interactions:

• Localization:

Database entries

• Structure:
  • 2M1C (N-terminal PAS domain of GdpP from Geobacillus thermodenitrificans) PubMed

• UniProt: P37484

• KEGG entry: [3]

• E.C. number:

Expression and regulation

• Operon: yybS-gdpP-rplI (according to DBTBS)

• Expression browser: gdpP PubMed

• Sigma factor:

• Regulation:

• Regulatory mechanism:

• Additional information:
  • there is an internal SigD-dependent antisense transcript (as-gdpP) PubMed

Biological materials

• Mutant:
  • GP998 (gdpP::spc), available in Jörg Stülke's lab

• Expression vector:

• lacZ fusion:

• GFP fusion:

• two-hybrid system:

• Antibody:

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)