› 3rdr

X-ray diffraction
2.2Å resolution

Structure of the catalytic domain of XlyA

Released:
DOI: 10.2210/pdb3rdr/pdb
PDB entry 3rdr coloured by chain, front view.
PDB entry 3rdr coloured by chain, side view.
PDB entry 3rdr coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
Role of net charge on catalytic domain and influence of cell wall binding domain on bactericidal activity, specificity, and host range of phage lysins.
Low LY, Yang C, Perego M, Osterman A, Liddington R
J Biol Chem 286 34391-403 (2011)
PMID: 21816821

Function and Biology Details

Reaction catalysed: 
Hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo hexamer
Assembly name:
PDBe Complex ID:
PDB-CPX-153954 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
N-acetylmuramoyl-L-alanine amidase XlyA Chain: A
Molecule details ›
Chain: A
Length: 157 amino acids
Theoretical weight: 17.11 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli
UniProt:
  • Canonical: P39800 (Residues: 1-154; Coverage: 44%)
Gene names: BSU12810, xlyA
Sequence domains: N-acetylmuramoyl-L-alanine amidase
Structure domains: Peptidoglycan recognition protein-like

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 12.3.1
Spacegroup: P6322
Unit cell:
a: 96.7Å b: 96.7Å c: 114.3Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.219 0.219 0.235
Expression system: Escherichia coli

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Citations

16 review citations

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

5 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)
4 more