8GN6

Crystallization of Sialidase from Porphyromonas gingivalis

Summary for 8GN6

• Entry DOI: 10.2210/pdb8gn6/pdb
• Descriptor: Sialidase, UNKNOWN LIGAND, ... (4 entities in total)
• Functional Keywords: sialidase, carbohydrate
• Biological source: Porphyromonas gingivalis; More
• Total number of polymer chains: 3
• Total formula weight: 175382.63

Authors

Dong, W.B. (deposition date: 2022-08-23, release date: 2023-04-19, Last modification date: 2024-05-29)

Primary citation

Dong, W.B.,Jiang, Y.L.,Zhu, Z.L.,Zhu, J.,Li, Y.,Xia, R.,Zhou, K.
Structural and enzymatic characterization of the sialidase SiaPG from Porphyromonas gingivalis.
Acta Crystallogr.,Sect.F, 79:87-94, 2023

PubMed Abstract: The sialidases, which catalyze the hydrolysis of sialic acid from extracellular glycoconjugates, are a group of major virulence factors in various pathogenic bacteria. In Porphyromonas gingivalis, which causes human periodontal disease, sialidase contributes to bacterial pathogenesis via promoting the formation of biofilms and capsules, reducing the ability for macrophage clearance, and providing nutrients for bacterial colonization. Here, the crystal structure of the P. gingivalis sialidase SiaPG is reported at 2.1 Å resolution, revealing an N-terminal carbohydrate-binding domain followed by a canonical C-terminal catalytic domain. Simulation of the product sialic acid in the active-site pocket together with functional analysis enables clear identification of the key residues that are required for substrate binding and catalysis. Moreover, structural comparison with other sialidases reveals distinct features of the active-site pocket which might confer substrate specificity. These findings provide the structural basis for the further design and optimization of effective inhibitors to target SiaPG to fight against P. gingivalis-derived oral diseases.

PubMed: 36995120
DOI: 10.1107/S2053230X23001735

Experimental method

X-RAY DIFFRACTION (2.1 Å)