› 5ly7

X-ray diffraction
3.1Å resolution

Crystal structure of NagZ H174A mutant from Pseudomonas aeruginosa in complex with the inhibitor 2-acetamido-1,2-dideoxynojirimycin

Released:
DOI: 10.2210/pdb5ly7/pdb
PDB entry 5ly7 coloured by chain, front view.
PDB entry 5ly7 coloured by chain, side view.
PDB entry 5ly7 coloured by chain, top view.
Source organism: Pseudomonas aeruginosa PAO1
Primary publication:
Catalytic Cycle of the N-Acetylglucosaminidase NagZ from Pseudomonas aeruginosa.
Acebrón I, Mahasenan KV, De Benedetti S, Lee M, Artola-Recolons C, Hesek D, Wang H, Hermoso JA, Mobashery S
J Am Chem Soc 139 6795-6798 (2017)
PMID: 28482153

Function and Biology Details

Reaction catalysed: 
Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-191198 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Beta-hexosaminidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 352 amino acids
Theoretical weight: 38.25 KDa
Source organism: Pseudomonas aeruginosa PAO1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9HZK0 (Residues: 1-332; Coverage: 100%)
Gene names: PA3005, nagZ
Sequence domains: Glycosyl hydrolase family 3 N terminal domain
Structure domains: Glycoside hydrolase, family 3, N-terminal domain

Ligands and Environments

2 bound ligands:
Ligand PEG 2 x PEG
Ligand NOK 2 x NOK
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALBA BEAMLINE XALOC
Spacegroup: P21
Unit cell:
a: 65.14Å b: 66.93Å c: 74.06Å
α: 90° β: 98.57° γ: 90°
R-values:
R R work R free
0.221 0.217 0.291
Expression system: Escherichia coli

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Citations

4 review citations

Cell-Wall Recycling of the Gram-Negative Bacteria and the Nexus to Antibiotic Resistance.
Dik et al. (2018)
3 more