› 4mut

X-ray diffraction
2.25Å resolution

Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant in complex with D-Alanine

Released:
DOI: 10.2210/pdb4mut/pdb
PDB entry 4mut coloured by chain, front view.
PDB entry 4mut coloured by chain, side view.
PDB entry 4mut coloured by chain, top view.
Source organism: Enterococcus gallinarum
Primary publication:
Structural basis for the evolution of vancomycin resistance D,D-peptidases.
Meziane-Cherif D, Stogios PJ, Evdokimova E, Savchenko A, Courvalin P
Proc Natl Acad Sci U S A 111 5872-7 (2014)
PMID: 24711382

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-191657 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptidase M15B domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 211 amino acids
Theoretical weight: 24.77 KDa
Source organism: Enterococcus gallinarum
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9JN36 (Residues: 1-190; Coverage: 100%)
Gene names: EGM181_06555, GTI89_02115, HZY99_04425, NCTC12360_01404, P7E30_05555, vanXYc
Sequence domains: D-alanyl-D-alanine carboxypeptidase
Structure domains: Muramoyl-pentapeptide Carboxypeptidase; domain 2

Ligands and Environments

5 bound ligands:
Ligand ZN 2 x ZN
Ligand DAL 2 x DAL
Ligand CL 1 x CL
Ligand PE3 1 x PE3
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P1
Unit cell:
a: 44.674Å b: 45.214Å c: 63.014Å
α: 86.69° β: 77.2° γ: 63.88°
R-values:
R R work R free
0.162 0.161 0.185
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Molecular mechanisms of vancomycin resistance.
Stogios et al. (2020)
4 more

17 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)
16 more