› 4bxe

X-ray diffraction
2.95Å resolution

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

Released:
DOI: 10.2210/pdb4bxe/pdb
PDB entry 4bxe coloured by chain, front view.
PDB entry 4bxe coloured by chain, side view.
PDB entry 4bxe 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 octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-164324 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 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:
ANHYDROMURAMIC PEPTIDE Chains: C, D
Molecule details ›
Chains: C, D
Length: 6 amino acids
Theoretical weight: 790 Da
Source organism: synthetic construct

Ligands and Environments

2 bound ligands:
Ligand ACT 3 x ACT
Ligand PEG 2 x PEG
3 modified residues:
Ligand DGL 2 x DGL
Ligand API 2 x API
Ligand DAL 4 x DAL

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P41212
Unit cell:
a: 100.94Å b: 100.94Å c: 165.25Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.203 0.266
Expression system: Escherichia coli

Quick links

Citations

8 review citations

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

3 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)
2 more