Structural analysis of β-L-arabinobiose binding protein in the metabolic pathway of hydroxyproline-rich glycoproteins in Bifidobacterium longum.

Bifidobacterium longum is a symbiotic human gut bacterium that has a degradation system for beta-arabinooligosaccharides which are present in the hydroxyproline-rich glycoproteins of edible plants. Whereas microbial degradation systems for alpha-linked arabinofuranosyl carbohydrates have been extensively studied, little is understood about the degradation systems targeting beta-linked arabinofuranosyl carbohydrates. We functionally and structurally analyzed a substrate-binding protein (SBP) of a putative ABC transporter (BLLJ_0208) in the beta-arabinooligosaccharide degradation system. Thermal shift assays and isothermal titration calorimetry revealed that the SBP specifically bound Araf-beta1,2-Araf (beta-Ara2 ) with a Kd of 0.150 muM, but did not bind L-arabinose or methyl-beta-Ara2 . Therefore, the SBP was termed beta-arabinobiose binding protein (BABP). Crystal structures of BABP complexed with beta-Ara2 were determined at resolutions of up to 1.78 A. The findings showed that beta-Ara2 was bound to BABP within a short tunnel between two lobes as an alpha-anomeric form at its reducing end. BABP forms extensive interactions with beta-Ara2 , and its binding mode was unique among SBPs. A molecular dynamics simulation revealed that the closed conformation of substrate-bound BABP is stable, whereas substrate-free form can adopt a fully open and two distinct semi-open states. The importer system specific for beta-Ara2 may contribute to microbial survival in biological niches with limited amounts of digestible carbohydrates.