4P8U image
Entry Detail
PDB ID:
4P8U
Title:
The crystal structures of YKL-39 in the absence of chitooligosaccharides was solved to resolutions of 2.4 angstrom
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2014-04-01
Release Date:
2014-10-01
Method Details:
Experimental Method:
Resolution:
2.40 Å
R-Value Free:
0.24
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 41 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Chitinase-3-like protein 2
Chain IDs:A
Chain Length:371
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
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)
PMID: 25477513 DOI: 10.1074/jbc.M114.588905

Abstact

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.

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