Glycoside Hydrolase Family 121

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• Author: ^^^Kiyotaka Fujita^^^
• Responsible Curator: ^^^Shinya Fushinobu^^^

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Glycoside Hydrolase Family GH121
Clan	none
Mechanism	retaining
Active site residues	not known
CAZy DB link
https://www.cazy.org/GH121.html

Substrate specificities

This family of glycoside hydrolases contains β-L-arabinobiosidases, as demonstrated for HypBA2 from Bifidobacterium longum JCM 1217 [1]. HypBA2 liberates the disaccharide Arafβ1-2Araf (β-Ara₂, a substrate of the GH127 β-L-arabinofuranosidase from B. longum JCM 1217 [2]) from unmodified Arafβ1-2Arafβ1-2Arafβ-hydroxyproline (Ara₃-Hyp), but not Arafα1-3Arafβ1-2Arafβ1-2Arafβ-Hyp (Ara₄-Hyp) or Arafβ1-2Arafβ-Hyp (Ara₂-Hyp). HypBA2 directly liberates β-Ara₂ from hydroxyproline-rich glycoproteins (HRGPs) such as carrot extensin and potato lectin. The family members are only found from prokaryote genomes, such as bacteria and actinomycetes.

Kinetics and Mechanism

HypBA2 is a retaining enzyme. The stereochemical course of the reaction was shown by transglycosylation activity toward 1-alkanols, such as methanol; the resulting Arafβ1-2Arafβ-Me was identified by ¹H-NMR and ¹³C-NMR analysis [1].

Catalytic Residues

The catalytic residues are not known but three conserved residues (Glu373, Asp515, and Glu713 in B. longum HypBA2) are the candidates based on mutagenesis and structural comparison [3].

Three-dimensional structures

Figure 1: β-L-arabinobiosidase HypBA2 from Bifidobacterium longum. The catalytic (α/α)₆ barrel domain is in green.

The first solved 3-D structure was β-L-arabinobiosidase HypBA2 from Bifidobacterium longum (PDB 6M5A) [3]. The catalytic domain adops an (α/α)₆ barrel fold similar to GH142, GH63, GH78, GH94, and GH37 (Figure 1).

Family Firsts

First stereochemistry determination

Shown to be retaining for HypBA2 enzyme by product analysis of glycosyl transfer reactions to methanol [1].

First catalytic nucleophile identification

Predicted based on structural homology [3], but currently no experimental proof.

First general acid/base residue identification

Predicted based on structural homology [3], but currently no experimental proof.

First 3-D structure

β-L-arabinobiosidase HypBA2 from Bifidobacterium longum [3].

References

1. Fujita K, Sakamoto S, Ono Y, Wakao M, Suda Y, Kitahara K, and Suganuma T. (2011). Molecular cloning and characterization of a beta-L-Arabinobiosidase in Bifidobacterium longum that belongs to a novel glycoside hydrolase family. J Biol Chem. 2011;286(7):5143-50. DOI:10.1074/jbc.M110.190512 |
2. Fujita K, Takashi Y, Obuchi E, Kitahara K, and Suganuma T. (2011). Characterization of a novel β-L-Arabinofuranosidase in Bifidobacterium longum: functional elucidation of A DUF1680 family member. J Biol Chem. 2011;286(44):38079-38085. DOI:10.1074/jbc.M111.248690 |
3. Saito K, Viborg AH, Sakamoto S, Arakawa T, Yamada C, Fujita K, and Fushinobu S. (2020). Crystal structure of β-L-arabinobiosidase belonging to glycoside hydrolase family 121. PLoS One. 2020;15(6):e0231513. DOI:10.1371/journal.pone.0231513 |