Crystal structure of a secondary vitamin D 3 binding site of milk β‐lactoglobulin

β‐lactoglobulin (β‐LG), one of the most investigated proteins, is a major bovine milk protein with a predominantly β structure. The structural function of the only α‐helix with three turns at the C‐terminus is unknown. Vitamin D 3 binds to the central calyx formed by the β‐strands. Whether there are two vitamin D binding‐sites in each β‐LG molecule has been a subject of controversy. Here, we report a second vitamin D 3 binding site identified by synchrotron X‐ray diffraction (at 2.4 Å resolution). In the central calyx binding mode, the aliphatic tail of vitamin D 3 clearly inserts into the binding cavity, where the 3‐OH group of vitamin D 3 binds externally. The electron density map suggests that the 3‐OH group interacts with the carbonyl of Lys‐60 forming a hydrogen bond (2.97 Å). The second binding site, however, is near the surface at the C‐terminus (residues 136–149) containing part of an α‐helix and a β‐strand I with 17.91 Å in length, while the span of vitamin D 3 is about 12.51 Å. A remarkable feature of the second exosite is that it combines an amphipathic α‐helix providing nonpolar residues (Phe‐136, Ala‐139, and Leu‐140) and a β‐strand providing a nonpolar (Ile‐147) and a buried polar residue (Arg‐148). They are linked by a hydrophobic loop (Ala‐142, Leu‐143, Pro‐144, and Met‐145). Thus, the binding pocket furnishes strong hydrophobic force to stabilize vitamin D 3 binding. This finding provides a new insight into the interaction between vitamin D 3 and β‐LG, in which the exosite may provide another route for the transport of vitamin D 3 in vitamin D 3 fortified dairy products. Atomic coordinates for the crystal structure of β‐LG‐vitamin D 3 complex described in this work have been deposited in the PDB (access code 2GJ5). Proteins 2008. © 2007 Wiley‐Liss, Inc.