Characterization of five marine family 29 glycoside hydrolases reveals an α-L-fucosidase targeting specifically Fuc(<i>α</i>1,4)GlcNAc

Schultz‐Johansen, Mikkel; Stougaard, Peter; Svensson, Birte; Tezé, David

doi:10.1093/glycob/cwab132

Cited by 9 publications

(3 citation statements)

References 62 publications

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“…Ri GH29 2A belonging to cluster 2 showed preference for α1,2 Gal linkages and displayed transfucosylation activity, as also reported for FgFCO1 from Fusarium graminearum PH-1 belonging to the same cluster 14 , 35 , 56 , 57 . La GH29 3A and Rs GH29 3A belonging to cluster 3 showed highest activity towards pNP-Fuc but no significant activity was found towards α1,2/3/4/6 fucosylated substrates, as also reported for Fp251, Fp239 and Fp231 from Paraglaciecola sp 58 , Alf1_Wf from W. fucaniytia CZ1127 T38 and ATCC_03833 3A from R. gnavus ATCC 29149 11 found in the same cluster. Ny GH29 4A belonging to cluster 4 showed preference for Fucα1,2 Gal, consistent with Fucosidase O from Omnitrophica bacterium OLB16 59 , HsFucA1 9 and Hs FucA2 60 from Homo sapiens found in the same cluster.…”

Section: Discussionsupporting

confidence: 71%

Exploring the sequence-function space of microbial fucosidases

Martínez Gascueña,

Wu,

Wang

et al. 2024

Commun Chem

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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.

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Section: Discussionsupporting

confidence: 71%

Exploring the sequence-function space of microbial fucosidases

Martínez Gascueña,

Wu,

Wang

et al. 2024

Commun Chem

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“…TT1817 and TT4187 belonging to cluster 3 showed highest activity towards pNP-Fuc but no signi cant activity was found towards α1,2/3/4/6 fucosylated substrates, as also reported for Fp251, Fp239 and Fp231 from Paraglaciecola sp. 53 , Alf1_Wf from W. fucaniytia CZ1127 T34 and ATCC_03833 from R. gnavus ATCC 29149 10 found in the same cluster. TT4225 belonging to cluster 4 showed preference for Fucα1,2Gal, consistent with Fucosidase O from Omnitrophica bacterium OLB16 54 , HsFucA1 55 and HsFucA2 56 from Homo sapiens found in the same cluster.…”

Section: Discussionmentioning

confidence: 79%

Exploring the sequence-function space of microbial fucosidases

Juge

Gascueña

et al. 2023

Preprint

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Microbial α-l-fucosidases catalyse the hydrolysis of terminal α-l-fucosidic linkages with diverse substrate/linkage specificities and can be used in transglycosylation reactions to synthesise oligosaccharides. Based on sequence identity, α-l-fucosidases have been classified in distinct glycoside hydrolases (GHs) families in the carbohydrate-active enzymes (CAZy) database. Here, we explored the sequence-function space of fucosidases from GH29 family. Based on sequence similarity network (SSN) analyses, 16 GH29 α-l-fucosidases were selected for functional characterisation. Using activity assays combined with HPAEC-PAD and LC-FD-MS/MS analyses, we determined the substrate and linkage specificities of these enzymes against a range of defined oligosaccharides and glycoconjugates, revealing a range of specificities for α1,2, α1,3, α1,4 and α1,6 linked fucosylated ligands. The structural basis for the substrate specificity of GH29 fucosidase from Bifidobacterium asteroides towards α1-6 linkages and FA2G2 N-glycan was further determined by X-ray crystallography and saturation transfer difference NMR. TLC combined with electrospray ionization – MS and NMR confirmed the capacity of this enzyme to carry out transfucosylation reactions with GlcNAc and Fuc1,3GlcNAc as acceptors. Taken together, these experimental data validate the use of SSN as a reliable bioinformatics approach to predict the substrate specificity and transfucosylation activity of GH29 fucosidases.

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“…Some functionally characterised bacterial GH29 fucosidases have only been reported to be active against artificial substrates, such as BF0810 from Bateroides fragilis NCTC 9343 [ 56 ], Fp240 and Fp251 from Paraglaciecola sp. [ 57 ]. Further investigation is required to determine their specificity towards natural substrates.…”

Section: Enzymatic and Structural Properties Of Fucosidasesmentioning

confidence: 99%

Structure and function of microbial α-l-fucosidases: a mini review

Owen

Juge

2023

Essays in Biochemistry

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Fucose is a monosaccharide commonly found in mammalian, insect, microbial and plant glycans. The removal of terminal α-l-fucosyl residues from oligosaccharides and glycoconjugates is catalysed by α-l-fucosidases. To date, glycoside hydrolases (GHs) with exo-fucosidase activity on α-l-fucosylated substrates (EC 3.2.1.51, EC 3.2.1.-) have been reported in the GH29, GH95, GH139, GH141 and GH151 families of the Carbohydrate Active Enzymes (CAZy) database. Microbes generally encode several fucosidases in their genomes, often from more than one GH family, reflecting the high diversity of naturally occuring fucosylated structures they encounter. Functionally characterised microbial α-l-fucosidases have been shown to act on a range of substrates with α-1,2, α-1,3, α-1,4 or α-1,6 fucosylated linkages depending on the GH family and microorganism. Fucosidases show a modular organisation with catalytic domains of GH29 and GH151 displaying a (β/α)8-barrel fold while GH95 and GH141 show a (α/α)6 barrel and parallel β-helix fold, respectively. A number of crystal structures have been solved in complex with ligands, providing structural basis for their substrate specificity. Fucosidases can also be used in transglycosylation reactions to synthesise oligosaccharides. This mini review provides an overview of the enzymatic and structural properties of microbial α-l-fucosidases and some insights into their biological function and biotechnological applications.

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Characterization of five marine family 29 glycoside hydrolases reveals an α-L-fucosidase targeting specifically Fuc(α1,4)GlcNAc

Cited by 9 publications

References 62 publications

Exploring the sequence-function space of microbial fucosidases

Exploring the sequence-function space of microbial fucosidases

Exploring the sequence-function space of microbial fucosidases

Structure and function of microbial α-l-fucosidases: a mini review

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