8P1S

Bifidobacterium asteroides alpha-L-fucosidase (TT1819) in complex with fucose.

8P1S の概要

• エントリーDOI: 10.2210/pdb8p1s/pdb
• 分子名称: Bifidobacterium asteroides alpha-L-fucosidase (TT1819), 1,2-ETHANEDIOL, alpha-L-fucopyranose, ... (7 entities in total)
• 機能のキーワード: glycosidase hydrolase, fucosidase, gh29, sugar binding protein
• 由来する生物種: Bifidobacterium asteroides
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 234971.92

構造登録者

Owen, C.D.,Penner, M.,Gascuena, A.N.,Wu, H.,Hernando, P.J.,Monaco, S.,Le Gall, G.,Gardner, R.,Ndeh, D.,Urbanowicz, P.A.,Spencer, D.I.R.,Walsh, M.A.,Angulo, J.,Juge, N. (登録日: 2023-05-12, 公開日: 2024-05-22, 最終更新日: 2025-06-04)

主引用文献

Martinez Gascuena, A.,Wu, H.,Wang, R.,Owen, C.D.,Hernando, P.J.,Monaco, S.,Penner, M.,Xing, K.,Le Gall, G.,Gardner, R.,Ndeh, D.,Urbanowicz, P.A.,Spencer, D.I.R.,Walsh, M.,Angulo, J.,Juge, N.
Exploring the sequence-function space of microbial fucosidases.
Commun Chem, 7:137-137, 2024

PubMed Abstract: Microbial α-L-fucosidases catalyse the hydrolysis of terminal α-L-fucosidic linkages and can perform transglycosylation reactions. Based on sequence identity, α-L-fucosidases are classified in glycoside hydrolases (GHs) families of the carbohydrate-active enzyme database. Here we explored the sequence-function space of GH29 fucosidases. Based on sequence similarity network (SSN) analyses, 15 GH29 α-L-fucosidases were selected for functional characterisation. HPAEC-PAD and LC-FD-MS/MS analyses revealed substrate and linkage specificities for α1,2, α1,3, α1,4 and α1,6 linked fucosylated oligosaccharides and glycoconjugates, consistent with their SSN clustering. The structural basis for the substrate specificity of GH29 fucosidase from Bifidobacterium asteroides towards α1,6 linkages and FA2G2 N-glycan was determined by X-ray crystallography and STD NMR. The capacity of GH29 fucosidases to carry out transfucosylation reactions with GlcNAc and 3FN as acceptors was evaluated by TLC combined with ESI-MS and NMR. These experimental data supported the use of SSN to further explore the GH29 sequence-function space through machine-learning models. Our lightweight protein language models could accurately allocate test sequences in their respective SSN clusters and assign 34,258 non-redundant GH29 sequences into SSN clusters. It is expected that the combination of these computational approaches will be used in the future for the identification of novel GHs with desired specificities.

PubMed: 38890439
DOI: 10.1038/s42004-024-01212-4

実験手法

X-RAY DIFFRACTION (1.9 Å)