darB [2020-07-09 15:22:27]

c-di-AMP binding protein

locus: BSU_14130

pI: 5.16

mw: 16.49 kDa

protein length: 147 aa

gene length: 444 bp

function: unknown

product: c-di-AMP binding protein

essential: no

synonyms: ykuL

Genomic Context

categories

• [category|SW 3|Information processing] → [category|SW 3.5|Targets of second messengers] → [category|SW 3.5.1|Targets of c-di-AMP]
• [category|SW 6|Groups of genes] → [category|SW 6.7|Proteins of unknown function]

Gene

Coordinates: 1,485,453 1,485,896

The protein

[SW|Domains]

• [SW|CBS domain] (aa 18-78) (according to UniProt)

Effectors of protein activity

• binds c-di-AMP [pubmed|31061098]

Structure

• [PDB|1YAV]

Expression and Regulation

Operons

• genes: [gene|A26502ADAC214D45A8F7F394587B0BDFBE7AF28E|ykuJ]-[gene|7FD784C885605F7FD27898BC9E83C28F21BE0E9D|ykuK]-[gene|899FF5BEE5D3F01778A0175E293EDBBDEB25717D|abbA]-[gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]-[gene|FE15A41A58A8177280817CA3825764C39185021A|ccpC]
  description: [Pubmed|16395550]

  regulatory mechanism

  • [protein|2C54FE2ADC82FF414D732018C90649D477A925AD|Spo0A]: activation, by [protein|2C54FE2ADC82FF414D732018C90649D477A925AD|Spo0A]~P [Pubmed|18840696,14651647], in [regulon|2C54FE2ADC82FF414D732018C90649D477A925AD|Spo0A regulon]
  • [protein|E39AFEB7B7F28969A35C4B51CC6E7819F71C79D9|CcpA]: repression, [Pubmed|16395550,12850135], in [regulon|E39AFEB7B7F28969A35C4B51CC6E7819F71C79D9|CcpA regulon]

  regulation

  • expressed under conditions that trigger sporulation ([SW|Spo0A]) [Pubmed|14651647]

Biological materials

Mutant

• MGNA-A773 (ykuL::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/773 NBRP B. subtilis, Japan]
• GP2769 (''Δ''''[gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]''::''ermC''), available in [SW|Jörg Stülke]'s lab
• BKE14130 (''ykuL''::''erm trpC2'') available in the Bacillus Genetic Stock Center and in [SW|Jörg Stülke]'s lab [pubmed|28189581]
• GP214 (deletion of ''[gene|A26502ADAC214D45A8F7F394587B0BDFBE7AF28E|ykuJ]-[gene|7FD784C885605F7FD27898BC9E83C28F21BE0E9D|ykuK]-[gene|899FF5BEE5D3F01778A0175E293EDBBDEB25717D|abbA]-[gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]'', replaced by ''aphA3''), available in [SW|Jörg Stülke]'s lab
• BKE14130 ([gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE14130 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATGTTTTCGACCCCTTTTC, downstream forward: _UP4_TAGGCTGTACGGTCCTATTT
• BKK14130 ([gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK14130 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATGTTTTCGACCCCTTTTC, downstream forward: _UP4_TAGGCTGTACGGTCCTATTT
• GP2800 (''Δ''''[gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]-[gene|FE15A41A58A8177280817CA3825764C39185021A|ccpC]]''::''phleo''), available in [SW|Jörg Stülke]'s lab

Expression vectors

• pGP2929 (N-terminal His-tag, purification from ''E. coli'', in [SW|pWH844]), available in [SW|Jörg Stülke]'s lab
• pGP635: expression of Strep-''ykuL'' by [SW|pGP380] in ''B. subtilis'' suitable for [SW|SPINE], available in [SW|Jörg Stülke]'s lab
• pGP767: expression of ''ykuL''-Strep by [SW|pGP382] in ''B. subtilis'' suitable for [SW|SPINE], available in [SW|Jörg Stülke]'s lab
• pGP3306: expression of ''ykuL'' by [SW|pBQ200] in ''B. subtilis'', available in [SW|Jörg Stülke]'s lab

two-hybrid system

• ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([SW|BACTH]), available in [SW|Jörg Stülke]'s lab

FLAG-tag construct

• GP2810 ''ykuL-3xFLAG spc'' (based on [SW|pGP1331]), available in [SW|Jörg Stülke]'s lab

labs

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

References

• 14651647,16395550,31061098,25215494,32603625