yukD

168

Ubiquitin-like protein, coordinates assembly of the type VII secretion machinery, putative bacteriocin

locus: BSU_31900

Molecular weight: 8.94 kDa

pI: 6.31

Protein length: 79 aa

Gene length: 240 bp

function: assembly of the type VII secretion machinery

product: ubiquitin-like protein, part of the type VII protein secretion system, putative bacteriocin

essential: no

synonyms: yukD

List of homologs in different organisms, belongs to COG5417 (Galperin et al., 2021)

Gene

Coordinates: 3,275,832  3,276,071

Phenotypes of a mutant

• loss of secretion of [protein|50D2A03E2D7B5D461540FD157377E0D37F771888|yukE] [Pubmed|24798022]

The protein

Catalyzed reaction/ biological activity

• export of [protein|A177DF098115F85F23A1D42EFB07D294B515830F|yfjA], [protein|50D2A03E2D7B5D461540FD157377E0D37F771888|yukE], [protein|75B0239578C92D4F3B298CBB077635BF5567C590|yxiB], [protein|2401A4E3E5E683472C51AB2F31BC4F54F672F32A|ywqH] [Pubmed|39436054,24828531,23861817,11973144]
• secretion and delivery of [wiki|LXG domain] toxins [pubmed|34280190]

Protein family

• EsaB family (single member, according to UniProt)

Structure

• [PDB|2BPS]
• [PDB|9QKS] (the [protein|3CC3E197848E9688413C15CEA7DDCF0A7120A920|yukD]-[protein|6007664F3D979B4D8D4662C7F6E5CF2F489268E3|yukB]-[protein|3FE4A91C7D0B43C8704391F2F9493852B3AED9B0|essB] complex) [pubmed|41270170]
• [AF|P71071]

Expression and Regulation

Operons

• genes: [gene|50D2A03E2D7B5D461540FD157377E0D37F771888|yukE]-[gene|3CC3E197848E9688413C15CEA7DDCF0A7120A920|yukD]-[gene|3FE4A91C7D0B43C8704391F2F9493852B3AED9B0|essB]-[gene|6007664F3D979B4D8D4662C7F6E5CF2F489268E3|yukB]-[gene|0A38B2E900532C9950DE6E629F5EB21D64E18B55|yueB]-[gene|DA52C4CD130F32734E01A52F2F395127D2260F61|yueC]-[gene|B258CA26B0EC2310475FCCD67F1F196857FC0004|yueD]

  description: [Pubmed|22383849]

  regulation

  • expressed in the stationary phase [Pubmed|23861817]
  • expression is reduced in motile cells as compared to non-motile cells [pubmed|33782055]

  regulatory mechanism

  • [protein|D343D2096664A972026D911E7A17A35C7B1CD1C9|degU]: activation, [protein|D343D2096664A972026D911E7A17A35C7B1CD1C9|degU]-P, [Pubmed|23861817], in [regulon|protein:D343D2096664A972026D911E7A17A35C7B1CD1C9|degU regulon]

  sigma factors

  • [protein|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|sigA]: sigma factor, [Pubmed|22383849], in [regulon|protein:360F48D576DE950DF79C1A2677B7A35A8D8CC30C|sigA regulon]

Biological materials

Mutant

• MGNA-A627 (yukD::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/627 NBRP B. subtilis, Japan]
• BKE31900 ([gene|3CC3E197848E9688413C15CEA7DDCF0A7120A920|yukD]::erm  trpC2) available at [http://bgsc.org/getdetail.php?bgscid=BKE31900 BGSC],  [Pubmed|28189581], upstream reverse: _UP1_CATTTAGGATCACCCTTACA,  downstream forward: _UP4_ATATTATGAAAGGATCTGGT
• BKK31900 ([gene|3CC3E197848E9688413C15CEA7DDCF0A7120A920|yukD]::kan  trpC2) available at [http://bgsc.org/getdetail.php?bgscid=BKK31900 BGSC],  [Pubmed|28189581], upstream reverse: _UP1_CATTTAGGATCACCCTTACA,  downstream forward: _UP4_ATATTATGAAAGGATCTGGT

References

Reviews

• 19155186,11973144,38957458

Original Publications

• 15576783,16845009,22383849,23861817,15978580,24798022,34280190,36154281,39436054,41270170