› 3d2y

X-ray diffraction
1.75Å resolution

Complex of the N-acetylmuramyl-L-alanine amidase AmiD from E.coli with the substrate anhydro-N-acetylmuramic acid-L-Ala-D-gamma-Glu-L-Lys

Released:
DOI: 10.2210/pdb3d2y/pdb
PDB entry 3d2y coloured by chain, front view.
PDB entry 3d2y coloured by chain, side view.
PDB entry 3d2y coloured by chain, top view.
Source organism: Escherichia coli str. K-12 substr. MG1655
Primary publication:
Specific structural features of the N-acetylmuramoyl-L-alanine amidase AmiD from Escherichia coli and mechanistic implications for enzymes of this family.
Kerff F, Petrella S, Mercier F, Sauvage E, Herman R, Pennartz A, Zervosen A, Luxen A, Frère JM, Joris B, Charlier P
J Mol Biol 397 249-59 (2010)
PMID: 20036252

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

Assemblies composition:
hetero dimer (preferred)
hetero tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-160002 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
N-acetylmuramoyl-L-alanine amidase AmiD Chain: A
Molecule details ›
Chain: A
Length: 261 amino acids
Theoretical weight: 29.38 KDa
Source organism: Escherichia coli str. K-12 substr. MG1655
Expression system: Escherichia coli
UniProt:
  • Canonical: P75820 (Residues: 18-276; Coverage: 100%)
Gene names: JW0851, amiD, b0867, ybjR
Sequence domains: N-acetylmuramoyl-L-alanine amidase
Structure domains:
Anhydro-N-acetylmuramic acid-L-Ala-D-gamma-Glu-L-Lys Chain: B
Molecule details ›
Chain: B
Length: 4 amino acids
Theoretical weight: 605 Da
Source organism: Escherichia coli str. K-12 substr. MG1655
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand GOL 2 x GOL
1 modified residue:
Ligand FGA 1 x FGA

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM30A
Spacegroup: P6122
Unit cell:
a: 88.274Å b: 88.274Å c: 181.834Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.209 0.207 0.253
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

The physiology of bacterial cell division.
Egan et al. (2013)
6 more

4 mentions without citation

Structure-function analysis of Staphylococcus aureus amidase reveals the determinants of peptidoglycan recognition and cleavage.
Büttner et al. (2014)
3 more