L,D-carboxypeptidase DacB and LdcB, and related proteins
This L,D-carboxypeptidase family includes LdcB LD-Carboxypeptidase from Streptococcus pneumoniae, Bacillus anthracis, and Bacillus subtilis, and L,D-carboxypeptidase DacB from Streptococcus pneumonia and Lactococcus lactis. These enzymes are active against cell-wall-derived tetrapeptides and synthetic tetrapeptides lacking the sugar moiety but are inactive against tetrapeptides terminating in L-alanine. L,D-carboxypeptidase DacB plays a key role in the remodeling of S. pneumoniae peptidoglycan during cell division. It adopts a zinc-dependent carboxypeptidase fold and acts as an L,D-carboxypeptidase towards the tetrapeptide L-Ala-D-iGln-L-Lys-D-Ala of the peptidoglycan stem. This family also includes vanY D-Ala-D-Ala carboxypeptidase which is vancomycin-inducible and penicillin-resistant. VanY hydrolyzes depsipeptide- and D-alanyl-D-alanine-containing peptidoglycan precursors; it is insensitive to beta-lactams. All these enzymes belong to the MEROPS family M15 subfamily B.
Feature 1: active site [active site], 5 residue positions
Conserved feature residue pattern:R H D [ED] H
Evidence:
Comment:based on structures of Bacillus anthracis LD-carboxypeptidase, Enterococcus faecalis D,D-dipeptidase VanXYg and Enterococcus faecium VanX, and on mutagenesis studies
Structure:4D0Y: Streptococcus pneumoniae LD-carboxypeptidase (DacB) binds zinc and phosphate ions; contacts at 4.0A
Jiyao W et al.(2023). "The conserved domain database in 2023.",