› 8t1y

X-ray diffraction
2.14Å resolution

Crystal Structure of Porphyromonas gingivalis Sialidase (PG_0352) Bound to Neu5Ac2en (DANA)

Released:
DOI: 10.2210/pdb8t1y/pdb
PDB entry 8t1y coloured by chain, front view.
PDB entry 8t1y coloured by chain, side view.
PDB entry 8t1y coloured by chain, top view.
Source organism: Porphyromonas gingivalis
Primary publication:
Functional and structural analyses reveal that a dual domain sialidase protects bacteria from complement killing through desialylation of complement factors.
Clark ND, Pham C, Kurniyati K, Sze CW, Coleman L, Fu Q, Zhang S, Malkowski MG, Li C
OpenAccess logo PLoS Pathog 19 e1011674 (2023)
PMID: 37747935

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:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-231395 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
exo-alpha-sialidase Chain: A
Molecule details ›
Chain: A
Length: 509 amino acids
Theoretical weight: 56.54 KDa
Source organism: Porphyromonas gingivalis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7MX62 (Residues: 31-526; Coverage: 94%)
Gene name: PG_0352
Sequence domains: BNR repeat-like domain

Ligands and Environments

4 bound ligands:
Ligand DAN 1 x DAN
Ligand PGE 2 x PGE
Ligand PEG 3 x PEG
Ligand PG4 1 x PG4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P21
Unit cell:
a: 80.517Å b: 55.9Å c: 84.478Å
α: 90° β: 115.49° γ: 90°
R-values:
R R work R free
0.188 0.186 0.227
Expression system: Escherichia coli

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Citations

1 mention without citation

Functional and structural analyses reveal that a dual domain sialidase protects bacteria from complement killing through desialylation of complement factors.
Clark et al. (2023)