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 journalArticlepeer-review

7 Citations (Scopus)

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 (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.

Original languageEnglish
Pages (from-to)736-741
Number of pages6
JournalBiochemical and Biophysical Research Communications
Volume494
Issue number3-4
DOIs
Publication statusPublished - Dec 16 2017
Externally publishedYes

Keywords

  • Binding Sites
  • Chitin/chemistry
  • Chitinases/chemistry
  • Lysine/chemistry
  • Models, Chemical
  • Molecular Docking Simulation
  • Oligosaccharides/chemistry
  • Protein Binding
  • Protein Conformation
  • Pteris/enzymology
  • Thermodynamics

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