› 4ly4

X-ray diffraction
2.2Å resolution

Crystal structure of peptidoglycan deacetylase (HP0310) with Zinc from Helicobacter pylori

Released:
DOI: 10.2210/pdb4ly4/pdb
PDB entry 4ly4 coloured by chain, front view.
PDB entry 4ly4 coloured by chain, side view.
PDB entry 4ly4 coloured by chain, top view.
Source organism: Helicobacter pylori G27
Primary publication:
Characterization of the divalent metal binding site of bacterial polysaccharide deacetylase using crystallography and quantum chemical calculations.
Shaik MM, Bhattacharjee N, Bhattacharjee A, Field MJ, Zanotti G
Proteins 82 1311-8 (2014)
PMID: 24346839

Function and Biology Details

Reaction catalysed: 
Deacetylation of xylans and xylo-oligosaccharides
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110302 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptidoglycan deacetylase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 326 amino acids
Theoretical weight: 37.57 KDa
Source organism: Helicobacter pylori G27
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: B5ZA76 (Residues: 1-293; Coverage: 100%)
Gene names: HPG27_289, pgdA
Sequence domains: Polysaccharide deacetylase
Structure domains: Glycoside hydrolase/deacetylase

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM16
Spacegroup: I222
Unit cell:
a: 113.64Å b: 153.93Å c: 153.88Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.169 0.207
Expression system: Escherichia coli BL21

Quick links

Citations

1 citations in other articles

Effects of metal-ion replacement on pyrazinamidase activity: A quantum mechanical study.
Khadem-Maaref et al. (2017)