Difference between revisions of "GdpP"

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(References)
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* '''Domains:'''  
 
* '''Domains:'''  
** N-terminal domain that shares minimum sequence homology with Haem-binding Per-ARNT-Sim (PAS) domains {{PubMed|21257773}}
+
** N-terminal domain that shares minimum sequence homology with Haem-binding Per-ARNT-Sim (PAS) domains (80 aa) {{PubMed|21257773}}
 
** degenerate GGDEF domain (aa 173 - 301) {{PubMed|22211522}}
 
** degenerate GGDEF domain (aa 173 - 301) {{PubMed|22211522}}
 
** DHH/ DHHA1 phosphodiesterase domain {{PubMed|22211522}}
 
** DHH/ DHHA1 phosphodiesterase domain {{PubMed|22211522}}
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* '''Structure:'''
 
* '''Structure:'''
 +
** [http://www.rcsb.org/pdb/explore/explore.do?structureId=2M1C 2M1C] (N-terminal PAS domain of GdpP from ''Geobacillus thermodenitrificans'') {{PubMed|23504013}}
  
 
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37484 P37484]
 
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37484 P37484]
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=References=
 
=References=
'''Additional publications:''' {{PubMed|22211522,22956758}}
+
<pubmed> 19901023 21257773 21566650 23504013 22211522,22956758</pubmed>
<pubmed> 19901023 21257773 21566650 </pubmed>
 
 
==GdpP homologs in other organisms==
 
==GdpP homologs in other organisms==
 
<pubmed> 18502872  </pubmed>
 
<pubmed> 18502872  </pubmed>
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 13:27, 27 March 2013

  • 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
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

Brit Winnen, Eric Anderson, James L Cole, Glenn F King, Susan L Rowland
Role of the PAS sensor domains in the Bacillus subtilis sporulation kinase KinA.
J Bacteriol: 2013, 195(10);2349-58
[PubMed:23504013] [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)