yciB

putative L,D-transpeptidase

locus: BSU_03350

pI: 6.18

mw: 21.94 kDa

protein length: 194 aa

gene length: 585 bp

function: unknown

product: putative L,D-transpeptidase

essential: no

synonyms

Genomic Context

categories

• [category|SW 1|Cellular processes] → [category|SW 1.1|Cell envelope and cell division] → [category|SW 1.1.1|Cell wall synthesis] → [category|SW 1.1.1.1|Biosynthesis of peptidoglycan]
• [category|SW 2|Metabolism] → [category|SW 2.6|Additional metabolic pathways] → [category|SW 2.6.1|Biosynthesis of cell wall components] → [category|SW 2.6.1.1|Biosynthesis of peptidoglycan]
• [category|SW 6|Groups of genes] → [category|SW 6.2|Membrane proteins]

Gene

Coordinates: 365,170 365,754

The protein

Protein family

• YkuD family (with [protein|6F256986E591DB82974A7F54EB1CE0C024A6F63B|Ldt] and [protein|293794B65B9EEB7F049138F73893303BABFB9A2A|YqjB], according to UniProt)

Structure

• [PDB|4LZH] (from Klebsiella pneumoniae, 27% identity)

[SW|Localization]

• lipoprotein, cell membrane at the cell poles [Pubmed|20013255]

Expression and Regulation

Operons

• genes: [gene|93380E8EEB672C14C9BE2B5A6D8573FBCA149514|folEB]-[gene|456AF184261976FAA73359E81443F7035F457D07|yciB]-[gene|F735802BB483C2C5437240AB2E9FC340EAA5B353|yczL]-[gene|75DB07A2704FEC2932BD0CDD24E2B3454E9551E1|zagA]
  description: [Pubmed|9811636]

  sigma factors

  • [protein|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA]: sigma factor, [Pubmed|12426338], in [regulon|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA regulon]

  regulatory mechanism

  • [protein|A0CD8CCB54AE9F10DE3C876FB47B9877C303862D|Zur]: repression, in the presence of zinc [Pubmed|12426338], in [regulon|A0CD8CCB54AE9F10DE3C876FB47B9877C303862D|Zur regulon]

  regulation

  • [SW|folE2]: induced by zinc starvation ([protein|A0CD8CCB54AE9F10DE3C876FB47B9877C303862D|Zur]) [Pubmed|12426338]

Biological materials

Mutant

• MGNA-B998 (yciB::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/1997 NBRP B. subtilis, Japan]
• BKE03350 ([gene|456AF184261976FAA73359E81443F7035F457D07|yciB]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE03350 BGSC], [Pubmed|28189581], upstream reverse: _UP1_TGCAATAATGAATAATGAGA, downstream forward: _UP4_TGAATTGAAAACCGTTGACA
• BKK03350 ([gene|456AF184261976FAA73359E81443F7035F457D07|yciB]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK03350 BGSC], [Pubmed|28189581], upstream reverse: _UP1_TGCAATAATGAATAATGAGA, downstream forward: _UP4_TGAATTGAAAACCGTTGACA

References

• 12426338,20013255,9811636