Collect. Czech. Chem. Commun.
2008, 73, 608-615
https://doi.org/10.1135/cccc20080608
L-Fucose in Crystal Structures of IgG-Fc: Reinterpretation of Experimental Data
Petr Kolenkoa,b,*, Tereza Skálováa, Jan Dohnáleka and Jindřich Hašeka
a Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovského nám. 2, 162 06 Prague 6, Czech Republic
b Department of Solid State Engineering, Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University, Trojanova 13, 120 00 Prague 2, Czech Republic
Abstract
Glycosylation of IgG-Fc plays an important role in the activation of the immune system response. Effector functions are modulated by different degrees of deglycosylation of IgG-Fc. However, the geometry of oligosaccharides covalently bound to IgG-Fc does not seem to be in good agreement with electron density in most of the structures deposited in the Protein Data Bank. Our study of correlation between the oligosaccharide geometry, connectivity, and electron density shows several discrepancies, mainly for L-fucose. Revision of refinement of two structures containing the Fc-fragment solved at the highest resolution brings clear evidence for α-L-fucosylation instead of β-L-fucosylation as it was claimed in most of the deposited structures in the Protein Data Bank containing the Fc-fragment, and also in the original structures selected for re-refinement. Our revision refinement results in a decrease in R factors, better agreement with electron density, meaningful contacts, and acceptable geometry of L-fucose.
Keywords: Immunoglobulin; Fc-fragment; Fucose; Geometry.
References: 37 live references.
