6m5a | pdb_00006m5a

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

spinqualitylabelsall models 6m5a, resolution 1.85Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6m5a is a 1 chain structure with sequence from As 1.2186. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CA, EDO, PEG, PG4, PGE Gene: DWV93_04865 (AS 1.2186) Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Enzymes acting on alpha-L-arabinofuranosides have been extensively studied; however, the structures and functions of beta-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 beta-L-arabinooligosaccharides on plant hydroxyproline-rich glycoproteins. An extracellular beta-L-arabinobiosidase (HypBA2) belonging to the glycoside hydrolase (GH) family 121 plays a key role in the degradation pathway by releasing beta-1,2-linked arabinofuranose disaccharide (beta-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 A resolution. The HypBA2 structure consists of a central catalytic (alpha/alpha)6 barrel domain and two flanking (N- and C-terminal) beta-sandwich domains. A pocket in the catalytic domain appears to be suitable for accommodating the beta-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 alpha-glycosidase, GH94 chitobiose phosphorylase, GH142 beta-L-arabinofuranosidase, GH78 alpha-L-rhamnosidase, and GH37 alpha,alpha-trehalase. Based on these analyses, we concluded that the three conserved residues are essential for catalysis and substrate binding. beta-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 beta-Ara2 disaccharide on plant hydroxyproline-rich glycoproteins are shared in animal gut symbionts and plant pathogens. Crystal structure of beta-L-arabinobiosidase belonging to glycoside hydrolase family 121.,Saito K, Viborg AH, Sakamoto S, Arakawa T, Yamada C, Fujita K, Fushinobu S PLoS One. 2020 Jun 1;15(6):e0231513. doi: 10.1371/journal.pone.0231513., eCollection 2020. PMID:32479540 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

Proteopedia Page Contributors and Editors (what is this?)

OCA