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X-ray diffraction
1.7Å resolution

Trypanosoma rangeli Sialidase in Complex with 2-Keto-3-deoxy-D-glycero-D-galacto-2,3-difluoro-nononic acid (2,3-difluoro-KDN)

Released:
DOI: 10.2210/pdb2ags/pdb
PDB entry 2ags coloured by chain, front view.
PDB entry 2ags coloured by chain, side view.
PDB entry 2ags coloured by chain, top view.
Source organism: Trypanosoma rangeli
Primary publication:
Structural and kinetic analysis of two covalent sialosyl-enzyme intermediates on Trypanosoma rangeli sialidase.
Watts AG, Oppezzo P, Withers SG, Alzari PM, Buschiazzo A
J Biol Chem 281 4149-55 (2006)
PMID: 16298994

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:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129183 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Sialidase domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 652 amino acids
Theoretical weight: 71.21 KDa
Source organism: Trypanosoma rangeli
Expression system: Escherichia coli
UniProt:
  • Canonical: O44049 (Residues: 23-660; Coverage: 100%)
Sequence domains: BNR repeat-like domain
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand SO4 2 x SO4
Ligand FKD 1 x FKD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P212121
Unit cell:
a: 73.672Å b: 95.569Å c: 105.816Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.156 0.154 0.189
Expression system: Escherichia coli

Quick links

Citations

8 review citations

Mechanistic insights into glycosidase chemistry.
Vocadlo et al. (2008)
7 more

1 mention without citation

N-glycosylation modulates enzymatic activity of Trypanosoma congolense trans-sialidase.
Rosenau et al. (2022)