› 2vk5

X-ray diffraction
0.97Å resolution

THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES

Released:
DOI: 10.2210/pdb2vk5/pdb
PDB entry 2vk5 coloured by chain, front view.
PDB entry 2vk5 coloured by chain, side view.
PDB entry 2vk5 coloured by chain, top view.
Source organism: Clostridium perfringens
Primary publication:
The structure of Clostridium perfringens NanI sialidase and its catalytic intermediates.
Newstead SL, Potter JA, Wilson JC, Xu G, Chien CH, Watts AG, Withers SG, Taylor GL
J Biol Chem 283 9080-8 (2008)
PMID: 18218621

Function and Biology Details

Reaction catalysed: 
Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176792 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
exo-alpha-sialidase Chain: A
Molecule details ›
Chain: A
Length: 452 amino acids
Theoretical weight: 50.41 KDa
Source organism: Clostridium perfringens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q59310 (Residues: 243-694; Coverage: 65%)
Gene name: nanH
Sequence domains: BNR repeat-like domain
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand GOL 2 x GOL
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P212121
Unit cell:
a: 96.892Å b: 69.019Å c: 72.808Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.115 0.115 0.126
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Mucin glycan foraging in the human gut microbiome.
Tailford et al. (2015)
9 more

11 mentions without citation

Sialidases from gut bacteria: a mini-review.
Juge et al. (2016)
10 more