› 2vo9

X-ray diffraction
1.8Å resolution

CRYSTAL STRUCTURE OF THE ENZYMATICALLY ACTIVE DOMAIN OF THE LISTERIA MONOCYTOGENES BACTERIOPHAGE 500 ENDOLYSIN PLY500

Released:
DOI: 10.2210/pdb2vo9/pdb
PDB entry 2vo9 coloured by chain, front view.
PDB entry 2vo9 coloured by chain, side view.
PDB entry 2vo9 coloured by chain, top view.
Source organism: Listeria phage A500
Primary publication:
Structural analysis of the L-alanoyl-D-glutamate endopeptidase domain of Listeria bacteriophage endolysin Ply500 reveals a new member of the LAS peptidase family.
Korndörfer IP, Kanitz A, Danzer J, Zimmer M, Loessner MJ, Skerra A
Acta Crystallogr D Biol Crystallogr 64 644-50 (2008)
PMID: 18560152

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-174307 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
L-alanyl-D-glutamate peptidase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 179 amino acids
Theoretical weight: 19.79 KDa
Source organism: Listeria phage A500
Expression system: Escherichia coli
UniProt:
  • Canonical: Q37979 (Residues: 1-167; Coverage: 58%)
Gene names: ply, ply500
Sequence domains: D-alanyl-D-alanine carboxypeptidase
Structure domains: Muramoyl-pentapeptide Carboxypeptidase; domain 2

Ligands and Environments

2 bound ligands:
Ligand ZN 3 x ZN
Ligand SO4 6 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: C2221
Unit cell:
a: 59.787Å b: 95.18Å c: 182.578Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.196 0.244
Expression system: Escherichia coli

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Citations

5 review citations

Bacteriophage endolysins as novel antimicrobials.
Schmelcher et al. (2012)
4 more

10 mentions without citation

Genetic Dissection of the Type VI Secretion System in Acinetobacter and Identification of a Novel Peptidoglycan Hydrolase, TagX, Required for Its Biogenesis.
Weber et al. (2016)
9 more