PDBsum entry 2gj5

Transport protein

PDB id: 2gj5

Contents

Protein chain

161 a.a. *

Ligands

VD3 ×2

Waters ×38

* Residue conservation analysis

PDB id:

2gj5

Name:

Transport protein

Title:

Crystal structure of a secondary vitamin d3 binding site of milk beta- lactoglobulin

Structure:

Beta-lactoglobulin. Chain: a. Synonym: beta-lg, allergen bos d 5

Source:

Bos taurus. Cattle. Organism_taxid: 9913

Resolution:

2.40Å R-factor: 0.236 R-free: 0.298

Authors:

M.C.Yang,H.H.Guan,M.Y.Liu,J.M.Yang,W.L.Chen,C.J.Chen,S.J.Mao

Key ref:

M.C.Yang et al. (2008). Crystal structure of a secondary vitamin D3 binding site of milk beta-lactoglobulin. Proteins, 71, 1197-1210. PubMed id: 18004750 DOI: 10.1002/prot.21811

Date:

30-Mar-06 Release date: 02-Oct-07

Protein chain

P02754  (LACB_BOVIN) -  Beta-lactoglobulin from Bos taurus

Seq: 178 a.a.

Struc: 161 a.a.

DOI no: 10.1002/prot.21811

Proteins 71:1197-1210 (2008)

PubMed id: 18004750

Crystal structure of a secondary vitamin D3 binding site of milk beta-lactoglobulin.

M.C.Yang, H.H.Guan, M.Y.Liu, Y.H.Lin, J.M.Yang, W.L.Chen, C.J.Chen, S.J.Mao.

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).

Selected figure(s)

Figure 8.
Figure 8. Superimposed structure of the exosite before and after binding of vitamin D[3] and a diagram showing their contacts of less than 3.8 Å. (A) Superimposing the current model for vitamin D[3]- -LG (colored in gray) with previously described native -LG (in red) (PDB code 1BSQ) in the exosite reveals that the overall conformation is not substantially changed upon the binding of vitamin D[3]. (B) The exosite is near the surface of C-terminal -helix and -strand I, where the 3-OH group of vitamin D[3] does not apparently form hydrogen boding with -LG.

Figure 9.
Figure 9. Amphipathic helix of -LG and its interaction with vitamin D[3]. (A) The only -helix region of -LG is located between residues 130 and 141 (Fig. 1). Most interestingly, the -helix is oriented as amphipathic with all the charged residues clustered on one side without an exception. (B) The crystal structure reveals that the hydrophobic side of the -helix forms a stable hydrophobic pocket with -strand I. They are linked by a hydrophobic loop (residues 142-145) and thus facilitate the binding to vitamin D[3]. The stereo view shows that part of vitamin D[3] is near the surface, particularly for the aliphatic tail, which is consistent with that depicted in Figure 5.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 71, 1197-1210) copyright 2008.

Figures were selected by an automated process.