ldcB

LD-carboxypeptidase, releases D-Ala from the cell wall

locus: BSU_19620

pI: 5.84

mw: 30.70 kDa

protein length: 273 aa

gene length: 822 bp

function: cell wall synthesis

product: LD-carboxypeptidase

essential: no

synonyms: yodJ

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]

Gene

Coordinates: 2,134,566 2,135,387

The protein

Catalyzed reaction/ biological activity

• trimming of cell wall peptides (tetrapeptides to tripeptides) wit concomitant release of D-ala [Pubmed|24909784]

Protein family

• peptidase M15B family (single member, according to UniProt)

[SW|Cofactors]

• Zn²⁺ [Pubmed|24909784]

Structure

• [PDB|4OX3] [Pubmed|24909784]

[SW|Localization]

• extracellular (signal peptide) [Pubmed|18957862]

Expression and Regulation

Operons

• genes: [gene|3075327DBE55C4F628171AEE248CAED5870693FA|deoD]-[gene|9A22825FD67B6A205807433D0B4908F86E5AB343|ldcB]
  description: [Pubmed|22383849]

Biological materials

Mutant

• MGNA-B439 (yodJ::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/1438 NBRP B. subtilis, Japan]
• BKE19620 ([gene|9A22825FD67B6A205807433D0B4908F86E5AB343|ldcB]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE19620 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATATTACATTACCTTCCTT, downstream forward: _UP4_TAAAATGAAAAGCCCGCTTA
• BKK19620 ([gene|9A22825FD67B6A205807433D0B4908F86E5AB343|ldcB]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK19620 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATATTACATTACCTTCCTT, downstream forward: _UP4_TAAAATGAAAAGCCCGCTTA

References

• 18957862,24909784,22383849,21378199