› 4gyj

X-ray diffraction
1.65Å resolution

Crystal structure of mutant (D318N) bacillus subtilis family 3 glycoside hydrolase (nagz) in complex with glcnac-murnac (space group P1)

Released:
DOI: 10.2210/pdb4gyj/pdb
PDB entry 4gyj coloured by chain, front view.
PDB entry 4gyj coloured by chain, side view.
PDB entry 4gyj coloured by chain, top view.
Source organism: Bacillus subtilis subsp. subtilis str. 168
Primary publication:
Active site plasticity within the glycoside hydrolase NagZ underlies a dynamic mechanism of substrate distortion.
Bacik JP, Whitworth GE, Stubbs KA, Vocadlo DJ, Mark BL
Chem Biol 19 1471-82 (2012)
PMID: 23177201

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-154110 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Beta-hexosaminidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 648 amino acids
Theoretical weight: 71.23 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
Expression system: Escherichia coli
UniProt:
  • Canonical: P40406 (Residues: 18-642; Coverage: 100%)
Gene names: BSU01660, nagZ, ybbD, yzbA
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, MUB
Carbohydrate polymer
1 bound ligand:
Ligand NAG 2 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P1
Unit cell:
a: 58.45Å b: 73.39Å c: 83.43Å
α: 98.65° β: 110.14° γ: 92.43°
R-values:
R R work R free
0.164 0.163 0.19
Expression system: Escherichia coli

Quick links

Citations

6 review citations

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

5 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)
4 more