5YSD

Crystal structure of beta-1,2-glucooligosaccharide binding protein in complex with sophorotriose

Summary for 5YSD

• Entry DOI: 10.2210/pdb5ysd/pdb
• Descriptor: Lin1841 protein, beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-alpha-D-glucopyranose, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (5 entities in total)
• Functional Keywords: solute-binding protein, protein-carbohydrate complex, beta-1, 2-glucooligosaccharide, sophorooligosaccharide, alpha/beta domain, sugar binding protein
• Biological source: Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)
• Total number of polymer chains: 2
• Total formula weight: 90788.28

Authors

Abe, K.,Nakajima, M.,Taguchi, H.,Arakawa, T.,Fushinobu, S. (deposition date: 2017-11-14, release date: 2018-05-02, Last modification date: 2023-11-22)

Primary citation

Abe, K.,Sunagawa, N.,Terada, T.,Takahashi, Y.,Arakawa, T.,Igarashi, K.,Samejima, M.,Nakai, H.,Taguchi, H.,Nakajima, M.,Fushinobu, S.
Structural and thermodynamic insights into beta-1,2-glucooligosaccharide capture by a solute-binding protein inListeria innocua.
J. Biol. Chem., 293:8812-8828, 2018

PubMed Abstract: β-1,2-Glucans are bacterial carbohydrates that exist in cyclic or linear forms and play an important role in infections and symbioses involving Gram-negative bacteria. Although several β-1,2-glucan-associated enzymes have been characterized, little is known about how β-1,2-glucan and its shorter oligosaccharides (Sop s) are captured and imported into the bacterial cell. Here, we report the biochemical and structural characteristics of the Sop -binding protein (SO-BP, Lin1841) associated with the ATP-binding cassette (ABC) transporter from the Gram-positive bacterium Calorimetric analysis revealed that SO-BP specifically binds to Sop s with a degree of polymerization of 3 or more, with values in the micromolar range. The crystal structures of SO-BP in an unliganded open form and in closed complexes with tri-, tetra-, and pentaoligosaccharides (Sop) were determined to a maximum resolution of 1.6 Å. The binding site displayed shape complementarity to Sop , which adopted a zigzag conformation. We noted that water-mediated hydrogen bonds and stacking interactions play a pivotal role in the recognition of Sop by SO-BP, consistent with its binding thermodynamics. Computational free-energy calculations and a mutational analysis confirmed that interactions with the third glucose moiety of Sop s are significantly responsible for ligand binding. A reduction in unfavorable changes in binding entropy that were in proportion to the lengths of the Sop s was explained by conformational entropy changes. Phylogenetic and sequence analyses indicated that SO-BP ABC transporter homologs, glycoside hydrolases, and other related proteins are co-localized in the genomes of several bacteria. This study may improve our understanding of bacterial β-1,2-glucan metabolism and promote the discovery of unidentified β-1,2-glucan-associated proteins.

PubMed: 29678880
DOI: 10.1074/jbc.RA117.001536

Experimental method

X-RAY DIFFRACTION (2.1 Å)