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
Metabolic function and regulation of this protein in SubtiPathways: 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 This image was kindly provided by SubtiList
Expression at a glance   PubMed

Categories containing this gene/protein

metabolism of signalling nucleotides, membrane proteins

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

• BsubCyc: BSU40510

• 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:
  • two transmembrane domains at the N-terminus PubMed
  • a domain that shares minimum sequence homology with Heme-binding Per-ARNT-Sim (PAS) domains (80 aa) PubMed
  • degenerate GGDEF domain (aa 173 - 301) PubMed
  • DHH/ DHHA1 phosphodiesterase domain PubMed

• Modification:

• Cofactors:

• Effectors of protein activity:
  • ppGpp inhibits cyclic dinucleotide phosphodiesterase activity PubMed
  • Heme binding suppresses phosphodiesterase activity PubMed

• Interactions:

• Localization:

Database entries

• BsubCyc: BSU40510

• 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

Reviews

Fabian M Commichau, Achim Dickmanns, Jan Gundlach, Ralf Ficner, Jörg Stülke
A jack of all trades: the multiple roles of the unique essential second messenger cyclic di-AMP.
Mol Microbiol: 2015, 97(2);189-204
[PubMed:25869574] [WorldCat.org] [DOI] (I p)

Original publications

Carolina Gándara, Juan C Alonso
DisA and c-di-AMP act at the intersection between DNA-damage response and stress homeostasis in exponentially growing Bacillus subtilis cells.
DNA Repair (Amst): 2015, 27;1-8
[PubMed:25616256] [WorldCat.org] [DOI] (I p)

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)