› 2ber

X-ray diffraction
1.8Å resolution

Y370G Active Site Mutant of the Sialidase from Micromonospora viridifaciens in complex with beta-Neu5Ac (sialic acid).

Released:
DOI: 10.2210/pdb2ber/pdb
PDB entry 2ber coloured by chain, front view.
PDB entry 2ber coloured by chain, side view.
PDB entry 2ber coloured by chain, top view.
Source organism: Micromonospora viridifaciens
Primary publication:
Structure and mechanism of action of an inverting mutant sialidase.
Newstead S, Watson JN, Knoll TL, Bennet AJ, Taylor G
Biochemistry 44 9117-22 (2005)
PMID: 15966735

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-169775 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Sialidase Chain: A
Molecule details ›
Chain: A
Length: 601 amino acids
Theoretical weight: 64.19 KDa
Source organism: Micromonospora viridifaciens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q02834 (Residues: 47-647; Coverage: 99%)
Gene name: nedA
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand SLB 1 x SLB
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-3
Spacegroup: P21
Unit cell:
a: 55.44Å b: 49.535Å c: 107.041Å
α: 90° β: 101.74° γ: 90°
R-values:
R R work R free
0.143 0.14 0.199
Expression system: Escherichia coli BL21(DE3)

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Citations

3 review citations

Structural insights into sialic acid enzymology.
Buschiazzo et al. (2008)
2 more

1 mention without citation

Novel multi-component crystals of berberine with improved pharmaceutical properties.
Zhang et al. (2023)