› 3gsm

X-ray diffraction
2.4Å resolution

Vibrio cholerae family 3 glycoside hydrolase (NagZ) bound to N-Valeryl-PUGNAc

Released:
DOI: 10.2210/pdb3gsm/pdb
PDB entry 3gsm coloured by chain, front view.
PDB entry 3gsm coloured by chain, side view.
PDB entry 3gsm coloured by chain, top view.
Source organism: Vibrio cholerae
Primary publication:
Insight into a strategy for attenuating AmpC-mediated beta-lactam resistance: structural basis for selective inhibition of the glycoside hydrolase NagZ.
Balcewich MD, Stubbs KA, He Y, James TW, Davies GJ, Vocadlo DJ, Mark BL
Protein Sci 18 1541-51 (2009)
PMID: 19499593

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-192108 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Beta-hexosaminidase Chain: A
Molecule details ›
Chain: A
Length: 340 amino acids
Theoretical weight: 37.71 KDa
Source organism: Vibrio cholerae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9KU37 (Residues: 1-330; Coverage: 100%)
Gene names: VC_0692, 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 VPU 1 x VPU
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RUH2R
Spacegroup: P212121
Unit cell:
a: 47.98Å b: 86.44Å c: 86.44Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.209 0.272
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Bacterial cell-wall recycling.
Johnson et al. (2013)
6 more

3 mentions without citation

Insight into a strategy for attenuating AmpC-mediated beta-lactam resistance: structural basis for selective inhibition of the glycoside hydrolase NagZ.
Balcewich et al. (2009)
2 more