gdpP

168

c-di-AMP specific phosphodiesterase

locus: BSU_40510

Molecular weight: 74.14 kDa

pI: 4.86

Protein length: 659 aa

Gene length: 1980 bp

function: control of sporulation initiation, cell wall homeostasis

product: c-di-AMP phosphodiesterase

essential: no

synonyms: gdpP, yybT

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

Gene

Coordinates: 4,163,643  4,165,622

Phenotypes of a mutant

• inactivation of ''[gene|9B624751E8BD3EA616B4B50633A558F4CE032E2C|gdpP]'' strongly restores beta-lactam resistance in a ''[gene|081DF3EE9FA56209D648C7677188C61CE3AA8E41|sigM]'' mutant [Pubmed|22211522]
• a ''[gene|9B624751E8BD3EA616B4B50633A558F4CE032E2C|gdpP] [gene|8D0885839CD60C05FB806BBF08AFA05225E83B12|pgpH]'' double mutant acquires suppressor mutations in ''[gene|AFE2A9998219162FE32E95628B3CA9071099B61A|cdaA]'' [Pubmed|26240071]
• a ''[gene|9B624751E8BD3EA616B4B50633A558F4CE032E2C|gdpP] [gene|8D0885839CD60C05FB806BBF08AFA05225E83B12|pgpH]'' double mutant is defective in [wiki|biofilm formation] [Pubmed|27252699]
• altered morphology on MSgg medium [pubmed|29588402]

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The protein

Catalyzed reaction/ biological activity

• cyclic dinucleotide phosphodiesterase, hydrolysis of cyclic di-AMP [Pubmed|19901023]
• 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)

[wiki|Domains]

• two transmembrane domains at the N-terminus [Pubmed|19901023]
• a domain that shares minimum sequence homology with Heme-binding [PAS domain|Per-ARNT-Sim (PAS) domains] (80 aa) [Pubmed|21257773]
• degenerate [wiki|GGDEF domain] (aa 173 - 301) [Pubmed|19901023]
• a [wiki|DHH-DHHA1 domain] [Pubmed|19901023]

Structure

• [PDB|2M1C] (N-terminal PAS domain of GdpP from ''Geobacillus thermodenitrificans'') [Pubmed|23504327]
• [AF|P37484]

Effectors of protein activity

• ppGpp inhibits cyclic dinucleotide phosphodiesterase activity [Pubmed|19901023]
• Heme binding suppresses phosphodiesterase activity [Pubmed|21257773]

[wiki|Localization]

• cell membrane (according to UniProt)

Expression and Regulation

Operons

• genes: [gene|6640C754249DD8E4E15889CC838F5D04A682BF58|yybS]-[gene|9B624751E8BD3EA616B4B50633A558F4CE032E2C|gdpP]-[gene|56737276B364EC0BC7391F1BA15F225C352ED905|rplI]

  description: [Pubmed|22383849]

  additional information

  • term-seq has identified a potential novel regulatory RNA element including an intrinsic transcription terminator upstream of ''yybS'' [Pubmed|27120414]
  • there is an [protein|7024E4162A6D827069F882FDEACA696EBC05DD40|sigD]-dependent antisense RNA ([gene|0098E3A710385B31987947E6206A89000CA32F55|S1559]) to [gene|9B624751E8BD3EA616B4B50633A558F4CE032E2C|gdpP] [pubmed|22956758]

Biological materials

Mutant

• MGNA-B834 (yybT::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/1833 NBRP B. subtilis, Japan]
• GP998 (''[gene|9B624751E8BD3EA616B4B50633A558F4CE032E2C|gdpP]''::''spc''), available in [wiki|Jörg Stülke]'s lab [Pubmed|23192352]
• GP2040 (''[gene|9B624751E8BD3EA616B4B50633A558F4CE032E2C|gdpP]''::''spc'' ''[gene|8D0885839CD60C05FB806BBF08AFA05225E83B12|pgpH]''::''erm'' without terminator, available in [wiki|Jörg Stülke]'s lab) [Pubmed|26240071]
• BKE40510 ([gene|9B624751E8BD3EA616B4B50633A558F4CE032E2C|gdpP]::erm  trpC2) available at [http://bgsc.org/getdetail.php?bgscid=BKE40510 BGSC],  [Pubmed|28189581], upstream reverse: _UP1_CATTTCTATCACTCCCCACC,  downstream forward: _UP4_AGATGAAGGTTATTTTCTTA
• BKK40510 ([gene|9B624751E8BD3EA616B4B50633A558F4CE032E2C|gdpP]::kan  trpC2) available at [http://bgsc.org/getdetail.php?bgscid=BKK40510 BGSC],  [Pubmed|28189581], upstream reverse: _UP1_CATTTCTATCACTCCCCACC,  downstream forward: _UP4_AGATGAAGGTTATTTTCTTA

labs

• [wiki|Jörg Stülke], University of Göttingen, Germany [http://genmibio.uni-goettingen.de Homepage]

References

Reviews

• 25869574,26773214,30224435,32472931,32603625,36026528,37954098

Original Publications

• 19901023,21257773,21566650,23504327,22211522,22956758,25616256,26240071,27252699,29588402,18502872

GdpP homologs in other organisms

• 18502872