› 4muq

X-ray diffraction
1.36Å resolution

Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg in complex with D-Ala-D-Ala phosphinate analog

Released:
DOI: 10.2210/pdb4muq/pdb
PDB entry 4muq coloured by chain, front view.
PDB entry 4muq coloured by chain, side view.
PDB entry 4muq coloured by chain, top view.
Source organism: Enterococcus faecalis
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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-191889 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptidase M15B domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 255 amino acids
Theoretical weight: 29.59 KDa
Source organism: Enterococcus faecalis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9KHL8 (Residues: 1-254; Coverage: 100%)
Gene names: vanXYG, vanYG2
Sequence domains: D-alanyl-D-alanine carboxypeptidase
Structure domains:

Ligands and Environments

6 bound ligands:
Ligand ZN 1 x ZN
Ligand LY0 1 x LY0
Ligand 2D8 1 x 2D8
Ligand EDO 1 x EDO
Ligand GOL 2 x GOL
Ligand PE3 4 x PE3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P21
Unit cell:
a: 38.895Å b: 43.728Å c: 80.236Å
α: 90° β: 99.2° γ: 90°
R-values:
R R work R free
0.163 0.162 0.185
Expression system: Escherichia coli BL21(DE3)

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Citations

6 review citations

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

3 mentions without citation

Structural basis for the evolution of vancomycin resistance D,D-peptidases.
Meziane-Cherif et al. (2014)
2 more