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

Masayuki Miyake, Tohru Terada (Corresponding Author), Michiko Shimokawa, Naohisa Sugimoto, Takatoshi Arakawa, Kentaro Shimizu, Kiyohiko Igarashi, Kiyotaka Fujita, Shinya Fushinobu (Corresponding Author)

Research output: Contribution to journalArticleScientificpeer-review

Abstract

Bifidobacterium longum is a symbiotic human gut bacterium that has a degradation system for β-arabinooligosaccharides, which are present in the hydroxyproline-rich glycoproteins of edible plants. Whereas microbial degradation systems for α-linked arabinofuranosyl carbohydrates have been extensively studied, little is understood about the degradation systems targeting β-linked arabinofuranosyl carbohydrates. We functionally and structurally analyzed a substrate-binding protein (SBP) of a putative ABC transporter (BLLJ_0208) in the β-arabinooligosaccharide degradation system. Thermal shift assays and isothermal titration calorimetry revealed that the SBP specifically bound Araf-β1,2-Araf (β-Ara2) with a Kd of 0.150 μm, but did not bind L-arabinose or methyl-β-Ara2. Therefore, the SBP was termed β-arabinobiose-binding protein (BABP). Crystal structures of BABP complexed with β-Ara2 were determined at resolutions of up to 1.78 Å. The findings showed that β-Ara2 was bound to BABP within a short tunnel between two lobes as an α-anomeric form at its reducing end. BABP forms extensive interactions with β-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 β-Ara2 may contribute to microbial survival in biological niches with limited amounts of digestible carbohydrates. Database: Atomic coordinates and structure factors (codes 6LCE and 6LCF) have been deposited in the Protein Data Bank (http://wwpdb.org/).

Original languageEnglish
Number of pages16
JournalFEBS Journal
Early online date4 Apr 2020
DOIs
Publication statusE-pub ahead of print - 4 Apr 2020
MoE publication typeA1 Journal article-refereed

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Keywords

  • ABC transporter
  • human gut bacterium
  • isothermal titration calorimetry
  • molecular dynamics simulation
  • substrate-binding protein

Cite this

Miyake, M., Terada, T., Shimokawa, M., Sugimoto, N., Arakawa, T., Shimizu, K., Igarashi, K., Fujita, K., & Fushinobu, S. (2020). Structural analysis of β-L-arabinobiose-binding protein in the metabolic pathway of hydroxyproline-rich glycoproteins in Bifidobacterium longum. FEBS Journal. https://doi.org/10.1111/febs.15315