› 5fre

X-ray diffraction
1.9Å resolution

Characterization of a novel CBM from Clostridium perfringens

Released:
DOI: 10.2210/pdb5fre/pdb
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PDB entry 5fre coloured by chain, front view.
PDB entry 5fre coloured by chain, side view.
PDB entry 5fre coloured by chain, top view.
Source organism: Clostridium perfringens
Primary publication:
Characterization of a high-affinity sialic acid-specific CBM40 from Clostridium perfringens and engineering of a divalent form.
Ribeiro JP, Pau W, Pifferi C, Renaudet O, Varrot A, Mahal LK, Imberty A
Biochem J 473 2109-18 (2016)
PMID: 27208171

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:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-101670 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
exo-alpha-sialidase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 194 amino acids
Theoretical weight: 22.1 KDa
Source organism: Clostridium perfringens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0H2YQR1 (Residues: 48-236; Coverage: 27%)
Gene names: CPF_0721, nanI
Sequence domains: Sialidase, N-terminal domain
Structure domains: Jelly Rolls

Ligands and Environments

Carbohydrate polymer : NEW Components: GAL, SIA
Carbohydrate polymer
3 bound ligands:
Ligand CA 8 x CA
Ligand 1PG 2 x 1PG
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ESRF BEAMLINE BM30A
Spacegroup: P21
Unit cell:
a: 64.348Å b: 76.714Å c: 67.254Å
α: 90° β: 93.46° γ: 90°
R-values:
R R work R free
0.175 0.173 0.209
Expression system: Escherichia coli BL21(DE3)

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Citations

4 review citations

Lectin engineering: the possible and the actual.
Hirabayashi et al. (2019)
3 more

1 mention without citation

Tailor-made Janus lectin with dual avidity assembles glycoconjugate multilayers and crosslinks protocells.
Ribeiro et al. (2018)

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