› 4knl

X-ray diffraction
1.55Å resolution

Crystal structure of Staphylococcus aureus hydrolase AmiA in complex with its ligand

Released:
DOI: 10.2210/pdb4knl/pdb
Model geometry
Fit model/data
PDB entry 4knl coloured by chain, front view.
PDB entry 4knl coloured by chain, side view.
PDB entry 4knl coloured by chain, top view.
Source organisms:
Primary publication:
Structure-function analysis of Staphylococcus aureus amidase reveals the determinants of peptidoglycan recognition and cleavage.
Büttner FM, Zoll S, Nega M, Götz F, Stehle T
J Biol Chem 289 11083-11094 (2014)
PMID: 24599952

Function and Biology Details

Reactions catalysed: 
an N(4)-(oligosaccharide-(1->3)-[oligosaccharide-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-alpha-D-GlcNAc)-L-asparaginyl-[protein] +H2O = an oligosaccharide-(1->3)-[oligosaccharide-(1->6)]-beta-D-Man-(1->4)-D-GlcNAc + N(4)-(N-acetyl-beta-D-glucosaminyl)-L-asparaginyl-[protein].
Hydrolyzes the link between N-acetylmuramoyl residues and L-amino acidresidues in certain cell-wall glycopeptides.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-164695 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Bifunctional autolysin Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 225 amino acids
Theoretical weight: 25.27 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q2FZK7 (Residues: 198-421; Coverage: 18%)
Gene names: SAOUHSC_00994, atl, nag
Sequence domains: N-acetylmuramoyl-L-alanine amidase
Structure domains: Peptidoglycan recognition protein-like
Muramyl tetrapeptide Chains: F, G
Molecule details ›
Chains: F, G
Length: 5 amino acids
Theoretical weight: 457 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

7 bound ligands:
Ligand IMD 4 x IMD
Ligand NA 8 x NA
Ligand FMT 2 x FMT
Ligand OXM 1 x OXM
Ligand MPD 1 x MPD
Ligand TAR 1 x TAR
Ligand MUB 2 x MUB
2 modified residues:
Ligand ALY 2 x ALY
Ligand DAL 2 x DAL

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21
Unit cell:
a: 67.81Å b: 82.83Å c: 77.43Å
α: 90° β: 96.18° γ: 90°
R-values:
R R work R free
0.172 0.171 0.198
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

4 review citations

Carbohydrate recognition and lysis by bacterial peptidoglycan hydrolases.
Alcorlo et al. (2017)
3 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