6M5A

Crystal structure of GH121 beta-L-arabinobiosidase HypBA2 from Bifidobacterium longum

Summary for 6M5A

• Entry DOI: 10.2210/pdb6m5a/pdb
• Descriptor: Beta-L-arabinobiosidase, DI(HYDROXYETHYL)ETHER, TRIETHYLENE GLYCOL, ... (7 entities in total)
• Functional Keywords: (alpha/alpha)6 barrel, glycoside hydrolase family 121, hydrolase
• Biological source: Bifidobacterium longum
• Total number of polymer chains: 1
• Total formula weight: 99329.40

Authors

Saito, K.,Arakawa, T.,Yamada, C.,Fujita, K.,Fushinobu, S. (deposition date: 2020-03-10, release date: 2020-06-03, Last modification date: 2024-03-27)

Primary citation

Saito, K.,Viborg, A.H.,Sakamoto, S.,Arakawa, T.,Yamada, C.,Fujita, K.,Fushinobu, S.
Crystal structure of beta-L-arabinobiosidase belonging to glycoside hydrolase family 121.
Plos One, 15:e0231513-e0231513, 2020

PubMed Abstract: Enzymes acting on α-L-arabinofuranosides have been extensively studied; however, the structures and functions of β-L-arabinofuranosidases are not fully understood. Three enzymes and an ABC transporter in a gene cluster of Bifidobacterium longum JCM 1217 constitute a degradation and import system of β-L-arabinooligosaccharides on plant hydroxyproline-rich glycoproteins. An extracellular β-L-arabinobiosidase (HypBA2) belonging to the glycoside hydrolase (GH) family 121 plays a key role in the degradation pathway by releasing β-1,2-linked arabinofuranose disaccharide (β-Ara2) for the specific sugar importer. Here, we present the crystal structure of the catalytic region of HypBA2 as the first three-dimensional structure of GH121 at 1.85 Å resolution. The HypBA2 structure consists of a central catalytic (α/α)6 barrel domain and two flanking (N- and C-terminal) β-sandwich domains. A pocket in the catalytic domain appears to be suitable for accommodating the β-Ara2 disaccharide. Three acidic residues Glu383, Asp515, and Glu713, located in this pocket, are completely conserved among all members of GH121; site-directed mutagenesis analysis showed that they are essential for catalytic activity. The active site of HypBA2 was compared with those of structural homologs in other GH families: GH63 α-glycosidase, GH94 chitobiose phosphorylase, GH142 β-L-arabinofuranosidase, GH78 α-L-rhamnosidase, and GH37 α,α-trehalase. Based on these analyses, we concluded that the three conserved residues are essential for catalysis and substrate binding. β-L-Arabinobiosidase genes in GH121 are mainly found in the genomes of bifidobacteria and Xanthomonas species, suggesting that the cleavage and specific import system for the β-Ara2 disaccharide on plant hydroxyproline-rich glycoproteins are shared in animal gut symbionts and plant pathogens.

PubMed: 32479540
DOI: 10.1371/journal.pone.0231513

Experimental method

X-RAY DIFFRACTION (1.85 Å)