4P8U

The crystal structures of YKL-39 in the absence of chitooligosaccharides was solved to resolutions of 2.4 angstrom

4P8U の概要

• エントリーDOI: 10.2210/pdb4p8u/pdb
• 関連するPDBエントリー: 4P8U 4P8V 4P8W
• 分子名称: Chitinase-3-like protein 2, SULFATE ION, DI(HYDROXYETHYL)ETHER, ... (4 entities in total)
• 機能のキーワード: chitinase 3-like protein 2, human ykl-39, family-18 chitinase, sugar binding protein
• 由来する生物種: Homo sapiens (Human)
• 細胞内の位置: Secreted : Q15782
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 41917.49

構造登録者

Suginta, W.,Ranok, A.,Robinson, R.C.,Wongsantichon, J. (登録日: 2014-04-01, 公開日: 2014-10-01, 最終更新日: 2024-11-20)

主引用文献

Ranok, A.,Wongsantichon, J.,Robinson, R.C.,Suginta, W.
Structural and Thermodynamic Insights into Chitooligosaccharide Binding to Human Cartilage Chitinase 3-like Protein 2 (CHI3L2 or YKL-39).
J.Biol.Chem., 290:2617-2629, 2015

PubMed Abstract: Four crystal structures of human YKL-39 were solved in the absence and presence of chitooligosaccharides. The structure of YKL-39 comprises a major (β/α)8 triose-phosphate isomerase barrel domain and a small α + β insertion domain. Structural analysis demonstrates that YKL-39 interacts with chitooligosaccharides through hydrogen bonds and hydrophobic interactions. The binding of chitin fragments induces local conformational changes that facilitate tight binding. Compared with other GH-18 members, YKL-39 has the least extended chitin-binding cleft, containing five subsites for sugars, namely (-3)(-2)(-1)(+1)(+2), with Trp-360 playing a prominent role in the sugar-protein interactions at the center of the chitin-binding cleft. Evaluation of binding affinities obtained from isothermal titration calorimetry and intrinsic fluorescence spectroscopy suggests that YKL-39 binds to chitooligosaccharides with Kd values in the micromolar concentration range and that the binding energies increase with the chain length. There were no significant differences between the Kd values of chitopentaose and chitohexaose, supporting the structural evidence for the five binding subsite topology. Thermodynamic analysis indicates that binding of chitooligosaccharide to YKL-39 is mainly driven by enthalpy.

PubMed: 25477513
DOI: 10.1074/jbc.M114.588905

実験手法

X-RAY DIFFRACTION (2.4 Å)