PDBsum entry 2gj5

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Transport protein PDB id
Protein chain
161 a.a. *
VD3 ×2
Waters ×38
* Residue conservation analysis
PDB id:
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
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
30-Mar-06     Release date:   02-Oct-07    
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Protein chain
Pfam   ArchSchema ?
P02754  (LACB_BOVIN) -  Beta-lactoglobulin
178 a.a.
161 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     transport   1 term 
  Biochemical function     small molecule binding     2 terms  


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.
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21360616 J.Loch, A.Polit, A.Górecki, P.Bonarek, K.Kurpiewska, M.Dziedzicka-Wasylewska, and K.Lewiński (2011).
Two modes of fatty acid binding to bovine β-lactoglobulin-crystallographic and spectroscopic studies.
  J Mol Recognit, 24, 341-349.
PDB codes: 3npo 3nq3 3nq9
19298386 M.C.Yang, N.C.Chen, C.J.Chen, C.Y.Wu, and S.J.Mao (2009).
Evidence for beta-lactoglobulin involvement in vitamin D transport in vivo--role of the gamma-turn (Leu-Pro-Met) of beta-lactoglobulin in vitamin D binding.
  FEBS J, 276, 2251-2265.  
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