6LCE

Crystal Structure of beta-L-arabinobiose binding protein - selenomethionine derivative

Summary for 6LCE

• Entry DOI: 10.2210/pdb6lce/pdb
• Descriptor: ABC transporter substrate binding component, beta-L-arabinofuranose-(1-2)-alpha-L-arabinofuranose (3 entities in total)
• Functional Keywords: substrate-binding protein of abc transporter, sugar binding protein
• Biological source: Bifidobacterium longum
• Total number of polymer chains: 1
• Total formula weight: 47200.44

Authors

Miyake, M.,Arakawa, T.,Fushinobu, S. (deposition date: 2019-11-18, release date: 2020-04-22, Last modification date: 2024-11-13)

Primary citation

Miyake, M.,Terada, T.,Shimokawa, M.,Sugimoto, N.,Arakawa, T.,Shimizu, K.,Igarashi, K.,Fujita, K.,Fushinobu, S.
Structural analysis of beta-L-arabinobiose-binding protein in the metabolic pathway of hydroxyproline-rich glycoproteins in Bifidobacterium longum.
Febs J., 287:5114-5129, 2020

PubMed 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-Ara ) with a K of 0.150 μm, but did not bind L-arabinose or methyl-β-Ara . Therefore, the SBP was termed β-arabinobiose-binding protein (BABP). Crystal structures of BABP complexed with β-Ara were determined at resolutions of up to 1.78 Å. The findings showed that β-Ara 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-Ara , 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-Ara 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/).

PubMed: 32246585
DOI: 10.1111/febs.15315

Experimental method

X-RAY DIFFRACTION (1.78 Å)