› 3nvd

X-ray diffraction
1.84Å resolution

Structure of YBBD in complex with pugnac

Released:
DOI: 10.2210/pdb3nvd/pdb
PDB entry 3nvd coloured by chain, front view.
PDB entry 3nvd coloured by chain, side view.
PDB entry 3nvd coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
Structural and kinetic analysis of Bacillus subtilis N-acetylglucosaminidase reveals a unique Asp-His dyad mechanism.
Litzinger S, Fischer S, Polzer P, Diederichs K, Welte W, Mayer C
J Biol Chem 285 35675-84 (2010)
PMID: 20826810

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:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-154110 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Beta-hexosaminidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 642 amino acids
Theoretical weight: 70.67 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli
UniProt:
  • Canonical: P40406 (Residues: 1-642; Coverage: 100%)
Gene names: BSU01660, nagZ, ybbD, yzbA
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand OAN 2 x OAN
Ligand PG4 1 x PG4
Ligand NA 2 x NA
Ligand ACT 4 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P1
Unit cell:
a: 58.473Å b: 73.206Å c: 83.788Å
α: 79.83° β: 69.45° γ: 88.22°
R-values:
R R work R free
0.191 0.187 0.246
Expression system: Escherichia coli

Quick links

Citations

12 review citations

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

7 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)
6 more