Identification of common structural features of binding sites in galactose‐specific proteins

Abstract

Galactose-binding proteins characterize an important subgroup of sugar-binding proteins that are involved in a variety of biological processes. Structural studies have shown that the Gal-specific proteins encompass a diverse range of primary and tertiary structures. The binding sites for galactose also seem to vary in different protein-galactose complexes. No common binding site features that are shared by the Gal-specific proteins to achieve ligand specificity are so far known. With the assumption that common recognition principles will exist for common substrate recognition, the present study was undertaken to identify and characterize any unique galactose-binding site signature by analyzing the three-dimensional (3D) structures of 18 protein-galactose complexes. These proteins belong to 7 nonhomologous families; thus, there is no sequence or structural similarity across the families. Within each family, the binding site residues and their relative distances were well conserved, but there were no similarities across families. A novel, yet simple, approach was adopted to characterize the binding site residues by representing their relative spatial dispositions in polar coordinates. A combination of the deduced geometrical features with the structural characteristics, such as solvent accessibility and secondary structure type, furnished a potential galactose-binding site signature. The signature was evaluated by incorporation into the program COTRAN to search for potential galactose-binding sites in proteins that share the same fold as the known galactose-binding proteins. COTRAN is able to detect galactose-binding sites with a very high specificity and sensitivity. The deduced galactose-binding site signature is strongly validated and can be used to search for galactose-binding sites in proteins. PROSITE-type signature sequences have also been inferred for galectin and C-type animal lectin-like fold families of Gal-binding proteins.

Crystal structure of lactose permease in complex with an affinity inactivator yields unique insight into sugar recognition

“…Moreover, E269 now directly coordinates the galactopyranosyl ring and a different type of stacking between the galactopyranosyl ring and W151 is observed. The new structure forms a parallel arrangement with the Trp ring, instead of the previously observed perpendicular stacking; both modes have been observed previously (18).…”

“…It is noteworthy that the β2-adrenerigic receptor, solved in complex with a disulfide-coupled ligand (17), also lacked density for the disulfide connection. Placement of the galactopyranosyl moiety was assisted by a number of observations: (i) The overall shape of the electron density peak imposes parallel stacking with the indole ring of W151, which is a common sugar-binding motif (18,19). (ii) The hydroxyls of the sugar are usually observed facing toward opposite sides of the Trp ring (18,19).…”

“…Placement of the galactopyranosyl moiety was assisted by a number of observations: (i) The overall shape of the electron density peak imposes parallel stacking with the indole ring of W151, which is a common sugar-binding motif (18,19). (ii) The hydroxyls of the sugar are usually observed facing toward opposite sides of the Trp ring (18,19). (iii) The galactopyranosyl moiety is positioned to coordinate the C-4 and C-6 OH to E269, a residue involved in sugar recognition and specificity (4).…”

“…The MTS-gal position is compatible with galactose binding even with modifications of residue 122. Third, all the residues identified biochemically to be essential for sugar binding and specificity are involved in the MTS-gal binding, and the sugar coordination pattern is a common sugar-binding motif (18,19). This wealth of biochemical evidence converges to indicate that the galactose moiety likely resides in a position similar to that occupied by the natural substrate, lactose, during the transport cycle.…”

“…S1 shows a Fo-Fo difference map of the sugar-binding site). Final positioning of the galactopyranosyl moiety was performed using several pieces of evidence: (i) the shape of the electron density provides a parallel stacking on W151 ring, which is a common sugar-binding motif (18,19); (ii) the stacking is always observed with the hydroxyls facing toward the opposite side of the tryptophan ring (18,19); and (iii) this positioning allows coordination of C-4 OH to E269, a residue involved in sugar recognition and specificity (4). A significant peak in the 2mFo-DFc density was observed on the cytoplasmic side near E130 and N204 and could not be attributed to the protein.…”