gdpP

gdpP
168

c-di-AMP specific phosphodiesterase

Locus
BSU_40510
Molecular weight
74.14 kDa
Isoelectric point
4.86
Protein length
659 aaSequenceBlast
Gene length
1980 bpSequenceBlast
Function
control of sporulation initiation, cell wall homeostasis
Product
c-di-AMP phosphodiesterase
Essential
no
Synonyms
gdpP, yybT
Outlinks
BsubCyc SubtiList UniProt STRING Genoscapist PaperBLAST

Genomic Context

Categories containing this gene/protein

List of homologs in different organisms, belongs to COG3887 (Galperin et al., 2021)

This gene is a member of the following regulons

Gene
Coordinates
4,163,643  4,165,622
Phenotypes of a mutant
inactivation of ''gdpP strongly restores beta-lactam resistance in a sigM'' mutant PubMed
a ''gdpP pgpH double mutant acquires suppressor mutations in cdaA'' PubMed
a ''gdpP pgpH'' double mutant is defective in biofilm formation PubMed
altered morphology on MSgg medium PubMed
The protein
Catalyzed reaction/ biological activity
cyclic dinucleotide phosphodiesterase, hydrolysis of cyclic di-AMP PubMed
3',3'-c-di-AMP + H2O --> 5'-O-phosphonoadenylyl-(3'→5')-adenosine + H+ (according to UniProt)
Protein family
GdpP/PdeA phosphodiesterase family (single member, according to UniProt)
Domains
two transmembrane domains at the N-terminus PubMed
a domain that shares minimum sequence homology with Heme-binding [PAS domain|Per-ARNT-Sim (PAS) domains] (80 aa) PubMed
degenerate GGDEF domain (aa 173 - 301) PubMed
a DHH-DHHA1 domain PubMed
Structure
5XT3 (PDB) (aa 318 ... 651, C-terminal DHH-DHH1 domain of GdpP from Staphylococcus aureus, 59.7% identity) PubMed
2M1C (PDB) (aa 57 ... 161, N-terminal PAS domain of GdpP from Geobacillus thermodenitrificans, 51% identity) PubMed
P37484 (AlphaFold)
Effectors of protein activity
ppGpp inhibits cyclic dinucleotide phosphodiesterase activity PubMed
Heme binding suppresses phosphodiesterase activity PubMed
Localization
cell membrane (according to UniProt)
Expression and Regulation
Operons
Genes
yybS-gdpP-rplI
Description
PubMed
Additional information
term-seq has identified a potential novel regulatory RNA element including an intrinsic transcription terminator upstream of yybS PubMed
there is an SigD-dependent antisense RNA (S1559) to gdpP PubMed
Open in new tab

yybS→rplI

2025-03-15 16:06:44

Jstuelk

133

5C9AFECBF28951E728207E104CAD078590852270

8A05783D8D0BA185AE37B5649C8B5E3E55F05A22

Biological materials
Mutant
MGNA-B834 (yybT::erm), available at the NBRP B. subtilis, Japan
GP998 (''gdpP::spc''), available in Jörg Stülke's lab PubMed
GP2040 (''gdpP::spc pgpH::erm'' without terminator, available in Jörg Stülke's lab) PubMed
BKE40510 (gdpP::erm  trpC2) available at BGSC,  PubMed, upstream reverse: _UP1_CATTTCTATCACTCCCCACC,  downstream forward: _UP4_AGATGAAGGTTATTTTCTTA
BKK40510 (gdpP::kan  trpC2) available at BGSC,  PubMed, upstream reverse: _UP1_CATTTCTATCACTCCCCACC,  downstream forward: _UP4_AGATGAAGGTTATTTTCTTA
Labs working on this gene/protein
Jörg Stülke, University of Göttingen, Germany Homepage
References
Reviews
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Original Publications
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GdpP homologs in other organisms
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9B624751E8BD3EA616B4B50633A558F4CE032E2C

Page visits: 5861

Time of last update: 2025-04-03 09:13:31

Author of last update: Jstuelk