Structural and thermodynamic insights into -1,2-glucooligosaccharide capture by a solute-binding protein in Listeria innocua

Koichi Abe, Naoki Sunagawa, Tohru Terada, Yuta Takahashi, Takatoshi Arakawa, Kiyohiko Igarashi, Masahiro Samejima, Hiroyuki Nakai, Hayao Taguchi, Masahiro Nakajima, Shinya Fushinobu

Research output: Contribution to journalArticleScientificpeer-review

7 Citations (Scopus)

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 (Sopns) are captured and imported into the bacterial cell. Here, we report the biochemical and structural characteristics of the Sopn-binding protein (SO-BP, Lin1841) associated with the ATP-binding cassette (ABC) transporter from the Gram-positive bacterium Listeria innocua. Calorimetric analysis revealed that SO-BP specifically binds to Sopns with a degree of polymerization of 3 or more, with Kd 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 (Sop3–5) were determined to a maximum resolution of 1.6 Å. The binding site displayed shape complementarity to Sopn, which adopted a zigzag conformation. We noted that water-mediated hydrogen bonds and stacking interactions play a pivotal role in the recognition of Sop3–5 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 Sopns are significantly responsible for ligand binding. A reduction in unfavorable changes in binding entropy that were in proportion to the lengths of the Sopns 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.

Original languageEnglish
Pages (from-to)8812-8828
Number of pages17
JournalJournal of Biological Chemistry
Volume293
Issue number23
DOIs
Publication statusPublished - 1 Jan 2018
MoE publication typeA1 Journal article-refereed

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Listeria
Glucans
Thermodynamics
Carrier Proteins
ATP-Binding Cassette Transporters
Entropy
Bacteria
Symbiosis
Glycoside Hydrolases
Gram-Negative Bacteria
Oligosaccharides
Metabolism
Polymerization
Free energy
Sequence Analysis
Conformations
Hydrogen
Hydrogen bonds
Proteins
Genes

Cite this

Abe, Koichi ; Sunagawa, Naoki ; Terada, Tohru ; Takahashi, Yuta ; Arakawa, Takatoshi ; Igarashi, Kiyohiko ; Samejima, Masahiro ; Nakai, Hiroyuki ; Taguchi, Hayao ; Nakajima, Masahiro ; Fushinobu, Shinya. / Structural and thermodynamic insights into -1,2-glucooligosaccharide capture by a solute-binding protein in Listeria innocua. In: Journal of Biological Chemistry. 2018 ; Vol. 293, No. 23. pp. 8812-8828.
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title = "Structural and thermodynamic insights into -1,2-glucooligosaccharide capture by a solute-binding protein in Listeria innocua",
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 (Sopns) are captured and imported into the bacterial cell. Here, we report the biochemical and structural characteristics of the Sopn-binding protein (SO-BP, Lin1841) associated with the ATP-binding cassette (ABC) transporter from the Gram-positive bacterium Listeria innocua. Calorimetric analysis revealed that SO-BP specifically binds to Sopns with a degree of polymerization of 3 or more, with Kd 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 (Sop3–5) were determined to a maximum resolution of 1.6 {\AA}. The binding site displayed shape complementarity to Sopn, which adopted a zigzag conformation. We noted that water-mediated hydrogen bonds and stacking interactions play a pivotal role in the recognition of Sop3–5 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 Sopns are significantly responsible for ligand binding. A reduction in unfavorable changes in binding entropy that were in proportion to the lengths of the Sopns 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.",
author = "Koichi Abe and Naoki Sunagawa and Tohru Terada and Yuta Takahashi and Takatoshi Arakawa and Kiyohiko Igarashi and Masahiro Samejima and Hiroyuki Nakai and Hayao Taguchi and Masahiro Nakajima and Shinya Fushinobu",
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Abe, K, Sunagawa, N, Terada, T, Takahashi, Y, Arakawa, T, Igarashi, K, Samejima, M, Nakai, H, Taguchi, H, Nakajima, M & Fushinobu, S 2018, 'Structural and thermodynamic insights into -1,2-glucooligosaccharide capture by a solute-binding protein in Listeria innocua', Journal of Biological Chemistry, vol. 293, no. 23, pp. 8812-8828. https://doi.org/10.1074/jbc.RA117.001536

Structural and thermodynamic insights into -1,2-glucooligosaccharide capture by a solute-binding protein in Listeria innocua. / Abe, Koichi; Sunagawa, Naoki; Terada, Tohru; Takahashi, Yuta; Arakawa, Takatoshi; Igarashi, Kiyohiko; Samejima, Masahiro; Nakai, Hiroyuki; Taguchi, Hayao; Nakajima, Masahiro; Fushinobu, Shinya.

In: Journal of Biological Chemistry, Vol. 293, No. 23, 01.01.2018, p. 8812-8828.

Research output: Contribution to journalArticleScientificpeer-review

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T1 - Structural and thermodynamic insights into -1,2-glucooligosaccharide capture by a solute-binding protein in Listeria innocua

AU - Abe, Koichi

AU - Sunagawa, Naoki

AU - Terada, Tohru

AU - Takahashi, Yuta

AU - Arakawa, Takatoshi

AU - Igarashi, Kiyohiko

AU - Samejima, Masahiro

AU - Nakai, Hiroyuki

AU - Taguchi, Hayao

AU - Nakajima, Masahiro

AU - Fushinobu, Shinya

PY - 2018/1/1

Y1 - 2018/1/1

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AB - 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 (Sopns) are captured and imported into the bacterial cell. Here, we report the biochemical and structural characteristics of the Sopn-binding protein (SO-BP, Lin1841) associated with the ATP-binding cassette (ABC) transporter from the Gram-positive bacterium Listeria innocua. Calorimetric analysis revealed that SO-BP specifically binds to Sopns with a degree of polymerization of 3 or more, with Kd 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 (Sop3–5) were determined to a maximum resolution of 1.6 Å. The binding site displayed shape complementarity to Sopn, which adopted a zigzag conformation. We noted that water-mediated hydrogen bonds and stacking interactions play a pivotal role in the recognition of Sop3–5 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 Sopns are significantly responsible for ligand binding. A reduction in unfavorable changes in binding entropy that were in proportion to the lengths of the Sopns 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.

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