› 4bxd

X-ray diffraction
3.1Å resolution

CRYSTAL STRUCTURE OF AMPDH3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH TETRASACCHARIDE PENTAPEPTIDE

Released:
DOI: 10.2210/pdb4bxd/pdb
PDB entry 4bxd coloured by chain, front view.
PDB entry 4bxd coloured by chain, side view.
PDB entry 4bxd coloured by chain, top view.
Source organisms:
Primary publication:
Cell-wall remodeling by the zinc-protease AmpDh3 from Pseudomonas aeruginosa.
Lee M, Artola-Recolons C, Carrasco-López C, Martínez-Caballero S, Hesek D, Spink E, Lastochkin E, Zhang W, Hellman LM, Boggess B, Hermoso JA, Mobashery S
J Am Chem Soc 135 12604-7 (2013)
PMID: 23931161

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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-164323 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
N-acetylmuramoyl-L-alanine amidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 255 amino acids
Theoretical weight: 28.76 KDa
Source organism: Pseudomonas aeruginosa PAO1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9I5D1 (Residues: 1-255; Coverage: 100%)
Gene names: PA0807, ampDh3
Sequence domains: N-acetylmuramoyl-L-alanine amidase
Structure domains:
PEPTIDE Chains: C, D
Molecule details ›
Chains: C, D
Length: 4 amino acids
Theoretical weight: 462 Da
Source organism: synthetic construct

Ligands and Environments

Carbohydrate polymer : NEW Components: MAG, NAG
Carbohydrate polymer
1 bound ligand:
Ligand ZN 2 x ZN
3 modified residues:
Ligand FGA 2 x FGA
Ligand 6CL 2 x 6CL
Ligand DAL 2 x DAL

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P41212
Unit cell:
a: 101.186Å b: 101.186Å c: 162.261Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.224 0.277
Expression system: Escherichia coli

Quick links

Citations

8 review citations

Ribosomally encoded antibacterial proteins and peptides from Pseudomonas.
Ghequire et al. (2014)
7 more

4 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)
3 more