Crystal structure and thermodynamic dissection of chitin oligosaccharide binding to the LysM module of chitinase-A from Pteris ryukyuensis

Takayuki Ohnuma; Toki Taira; Naoyuki Umemoto; Yoshihito Kitaoku; Morten Sørlie; Tomoyuki Numata; Tamo Fukamizo

doi:10.1016/j.bbrc.2017.08.143

Crystal structure and thermodynamic dissection of chitin oligosaccharide binding to the LysM module of chitinase-A from Pteris ryukyuensis

Takayuki Ohnuma, Toki Taira, Naoyuki Umemoto, Yoshihito Kitaoku, Morten Sørlie, Tomoyuki Numata, Tamo Fukamizo

Research output: Contribution to journal › Article › peer-review

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Abstract

We determined the crystal structure of a LysM module from Pteris ryukyuensis chitinase-A (PrLysM2) at a resolution of 1.8 Å. Structural and binding analysis of PrLysM2 indicated that this module recognizes chitin oligosaccharides in a shallow groove comprised of five sugar-binding subsites on one side of the molecule. The free energy changes (ΔG_r°) for binding of (GlcNAc)₆, (GlcNAc)₅, and (GlcNAc)₄ to PrLysM2 were determined to be −5.4, −5,4 and −4.6 kcal mol⁻¹, respectively, by ITC. Thermodynamic dissection of the binding energetics of (GlcNAc)₆ revealed that the driving force is the enthalpy change (ΔH_r° = −11.7 ± 0.2 kcal/mol) and the solvation entropy change (−TΔS_solv° = −5.9 ± 0.6 kcal/mol). This is the first description of thermodynamic signatures of a chitin oligosaccharide binding to a LysM module.

Original language	English
Pages (from-to)	736-741
Number of pages	6
Journal	Biochemical and Biophysical Research Communications
Volume	494
Issue number	3-4
DOIs	https://doi.org/10.1016/j.bbrc.2017.08.143
Publication status	Published - Dec 16 2017
Externally published	Yes

All Science Journal Classification (ASJC) codes

Biophysics
Biochemistry
Molecular Biology
Cell Biology

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title = "Crystal structure and thermodynamic dissection of chitin oligosaccharide binding to the LysM module of chitinase-A from Pteris ryukyuensis",

abstract = "We determined the crystal structure of a LysM module from Pteris ryukyuensis chitinase-A (PrLysM2) at a resolution of 1.8 {\AA}. Structural and binding analysis of PrLysM2 indicated that this module recognizes chitin oligosaccharides in a shallow groove comprised of five sugar-binding subsites on one side of the molecule. The free energy changes (ΔGr°) for binding of (GlcNAc)6, (GlcNAc)5, and (GlcNAc)4 to PrLysM2 were determined to be −5.4, −5,4 and −4.6 kcal mol−1, respectively, by ITC. Thermodynamic dissection of the binding energetics of (GlcNAc)6 revealed that the driving force is the enthalpy change (ΔHr° = −11.7 ± 0.2 kcal/mol) and the solvation entropy change (−TΔSsolv° = −5.9 ± 0.6 kcal/mol). This is the first description of thermodynamic signatures of a chitin oligosaccharide binding to a LysM module.",

author = "Takayuki Ohnuma and Toki Taira and Naoyuki Umemoto and Yoshihito Kitaoku and Morten S{\o}rlie and Tomoyuki Numata and Tamo Fukamizo",

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doi = "10.1016/j.bbrc.2017.08.143",

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T1 - Crystal structure and thermodynamic dissection of chitin oligosaccharide binding to the LysM module of chitinase-A from Pteris ryukyuensis

AU - Ohnuma, Takayuki

AU - Taira, Toki

AU - Umemoto, Naoyuki

AU - Kitaoku, Yoshihito

AU - Sørlie, Morten

AU - Numata, Tomoyuki

AU - Fukamizo, Tamo

PY - 2017/12/16

Y1 - 2017/12/16

N2 - We determined the crystal structure of a LysM module from Pteris ryukyuensis chitinase-A (PrLysM2) at a resolution of 1.8 Å. Structural and binding analysis of PrLysM2 indicated that this module recognizes chitin oligosaccharides in a shallow groove comprised of five sugar-binding subsites on one side of the molecule. The free energy changes (ΔGr°) for binding of (GlcNAc)6, (GlcNAc)5, and (GlcNAc)4 to PrLysM2 were determined to be −5.4, −5,4 and −4.6 kcal mol−1, respectively, by ITC. Thermodynamic dissection of the binding energetics of (GlcNAc)6 revealed that the driving force is the enthalpy change (ΔHr° = −11.7 ± 0.2 kcal/mol) and the solvation entropy change (−TΔSsolv° = −5.9 ± 0.6 kcal/mol). This is the first description of thermodynamic signatures of a chitin oligosaccharide binding to a LysM module.

AB - We determined the crystal structure of a LysM module from Pteris ryukyuensis chitinase-A (PrLysM2) at a resolution of 1.8 Å. Structural and binding analysis of PrLysM2 indicated that this module recognizes chitin oligosaccharides in a shallow groove comprised of five sugar-binding subsites on one side of the molecule. The free energy changes (ΔGr°) for binding of (GlcNAc)6, (GlcNAc)5, and (GlcNAc)4 to PrLysM2 were determined to be −5.4, −5,4 and −4.6 kcal mol−1, respectively, by ITC. Thermodynamic dissection of the binding energetics of (GlcNAc)6 revealed that the driving force is the enthalpy change (ΔHr° = −11.7 ± 0.2 kcal/mol) and the solvation entropy change (−TΔSsolv° = −5.9 ± 0.6 kcal/mol). This is the first description of thermodynamic signatures of a chitin oligosaccharide binding to a LysM module.

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Crystal structure and thermodynamic dissection of chitin oligosaccharide binding to the LysM module of chitinase-A from Pteris ryukyuensis

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