› 4oxd

X-ray diffraction
2.8Å resolution

Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition

Released:
DOI: 10.2210/pdb4oxd/pdb
PDB entry 4oxd coloured by chain, front view.
PDB entry 4oxd coloured by chain, side view.
PDB entry 4oxd coloured by chain, top view.
Source organisms:
Primary publication:
Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition.
Hoyland CN, Aldridge C, Cleverley RM, Duchêne MC, Minasov G, Onopriyenko O, Sidiq K, Stogios PJ, Anderson WF, Daniel RA, Savchenko A, Vollmer W, Lewis RJ
OpenAccess logo Structure 22 949-60 (2014)
PMID: 24909784

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-164961 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Peptidase M15B domain-containing protein Chains: A, B, C, D, E
Molecule details ›
Chains: A, B, C, D, E
Length: 187 amino acids
Theoretical weight: 21.2 KDa
Source organism: Streptococcus pneumoniae R6
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8DQQ1 (Residues: 56-238; Coverage: 84%)
Gene name: spr0554
Sequence domains: D-alanyl-D-alanine carboxypeptidase
Structure domains: Muramoyl-pentapeptide Carboxypeptidase; domain 2
MUB-ALA-ZGL-LYS-DSG Chain: H
Molecule details ›
Chain: H
Length: 4 amino acids
Theoretical weight: 461 Da
Source organism: Lactobacillus acidophilus

Ligands and Environments

5 bound ligands:
Ligand ZN 18 x ZN
Ligand MG 1 x MG
Ligand LYS 1 x LYS
Ligand CL 2 x CL
Ligand MUB 1 x MUB
1 modified residue:
Ligand DSG 1 x DSG

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: C2
Unit cell:
a: 345.954Å b: 42.549Å c: 79.318Å
α: 90° β: 93.07° γ: 90°
R-values:
R R work R free
0.276 0.273 0.334
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Carbohydrate recognition and lysis by bacterial peptidoglycan hydrolases.
Alcorlo et al. (2017)
3 more

3 mentions without citation

Cell Wall Hydrolases in Bacteria: Insight on the Diversity of Cell Wall Amidases, Glycosidases and Peptidases Toward Peptidoglycan.
Vermassen et al. (2019)
2 more