Crystal structure of a secondary vitamin D3 binding site of milk β‐lactoglobulin

2007/11/14 by Ming‐Chi Yang, Hong‐Hsiang Guan, Ming‐Yih Liu +5 · 1 voice · 99 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · Medicine · Nursing · #Binding site #Biochemistry #Biology #Chemistry #Crystallography #Digestive system and related health #Helix (gastropod) #Hydrogen bond #Hydrophobic effect #Infant Nutrition and Health #Molecule #Protein structure #Stereochemistry #Vitamin D Research Studies

paper · doi:10.1002/prot.21811

published in Proteins Structure Function and Bioinformatics 71(3), 1197-1210 (Wiley)

openalex publication_date 2007/11/14 · openalex created_date 2016/06/24 · openalex updated_date 2026/07/23

Abstract

Beta-lactoglobulin (beta-LG), one of the most investigated proteins, is a major bovine milk protein with a predominantly beta structure. The structural function of the only alpha-helix with three turns at the C-terminus is unknown. Vitamin D(3) binds to the central calyx formed by the beta-strands. Whether there are two vitamin D binding-sites in each beta-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 A 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 A). The second binding site, however, is near the surface at the C-terminus (residues 136-149) containing part of an alpha-helix and a beta-strand I with 17.91 A in length, while the span of vitamin D(3) is about 12.51 A. A remarkable feature of the second exosite is that it combines an amphipathic alpha-helix providing nonpolar residues (Phe-136, Ala-139, and Leu-140) and a beta-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 beta-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 beta-LG-vitamin D(3) complex described in this work have been deposited in the PDB (access code 2GJ5).

Citations

• PROCHECK: a program to check the stereochemical quality of protein structures

Cited by

• β-lactoglobulin's conformational requirements for ligand binding at the calyx and the dimer interphase: a flexible docking study. [europepmc]
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• Stabilization of Vitamin D in Pea Protein Isolate Nanoemulsions Increases Its Bioefficacy in Rats. [europepmc]
• In Silico Characterization of the Binding Modes of Surfactants with Bovine Serum Albumin. [europepmc]
• β-Lactoglobulin as a Nanotransporter for Glabridin: Exploring the Binding Properties and Bioactivity Influences. [europepmc]
• Alginate Trisaccharide Binding Sites on the Surface of β-Lactoglobulin Identified by NMR Spectroscopy: Implications for Molecular Network Formation. [europepmc]
• Isolation and Self-Association Studies of Beta-Lactoglobulin. [europepmc]
• Binding Sites for Oligosaccharide Repeats from Lactic Acid Bacteria Exopolysaccharides on Bovine β-Lactoglobulin Identified by NMR Spectroscopy. [europepmc]
• β-Lactoglobulin and Glycodelin: Two Sides of the Same Coin? [europepmc]
• Challenges and Advances in the Encapsulation of Bioactive Ingredients Using Whey Proteins. [europepmc]
• Computing the pH-Dependent Thermodynamics of the Allostery between Dimerization and Palmitate Binding in β-Lactoglobulin. [europepmc]
• Analysis of the mechanisms and efficiency of Taxifolin encapsulation in whey proteins via thermomechanical mixing and spray drying. [europepmc]
• Effects of galloyl group on the astringency perception of epigallocatechin gallate and epigallocatechin. [europepmc]

Discussions

• Bovine beta lactoglobulin angles, this is 2gj5.pdb. Showing an additional alternate site for the binding of vitamin D3. The most well known site is the first, enclosed one. The proposed second is more [bsky, 33 points, 1 comments]

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