PDBsum entry 1gx9

Lipocalin

PDB id: 1gx9

Contents

Protein chain

161 a.a. *

Ligands

REA

Waters ×139

* Residue conservation analysis

PDB id:

1gx9

Name:

Lipocalin

Title:

Bovine beta-lactoglobulin complexed with retinoic acid, trigonal lattice z

Structure:

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

Source:

Bos taurus. Bovine. Organism_taxid: 9913. Variant: genetic variant b. Organ: mammary gland. Other_details: protein purchased from sigma chemicals, cat.No. L8005

Biol. unit:

Dimer (from PDB file)

Resolution:

2.34Å R-factor: 0.227 R-free: 0.298

Authors:

G.Kontopidis,L.Sawyer

Key ref:

G.Kontopidis et al. (2002). The ligand-binding site of bovine beta-lactoglobulin: evidence for a function? J Mol Biol, 318, 1043-1055. PubMed id: 12054801 DOI: 10.1016/S0022-2836(02)00017-7

Date:

29-Mar-02 Release date: 13-Jun-02

Protein chain

P02754  (LACB_BOVIN) -  Beta-lactoglobulin from Bos taurus

Seq: 178 a.a.

Struc: 161 a.a.

DOI no: 10.1016/S0022-2836(02)00017-7

J Mol Biol 318:1043-1055 (2002)

PubMed id: 12054801

The ligand-binding site of bovine beta-lactoglobulin: evidence for a function?

G.Kontopidis, C.Holt, L.Sawyer.

ABSTRACT

Ever since the fortuitous observation that beta-lactoglobulin (beta-Lg), the major whey protein in the milk of ruminants, bound retinol, the details of the binding have been controversial. beta-Lg is a lipocalin, like plasma retinol-binding protein, so that ligand association was expected to make use of the central cavity in the protein. However, an early crystallographic analysis and some of the more recent solution studies indicated binding elsewhere. We have now determined the crystal structures of the complexes of the trigonal form of beta-Lg at pH 7.5 with bound retinol (R=21.4% for 7329 reflections between 20 and 2.4 A resolution, R(free)=30.6%) and with bound retinoic acid (R=22.7% for 7813 reflections between 20 and 2.34 A resolution, R(free)=29.8%). Both ligands are found to occupy the central calyx in a manner similar to retinol binding in retinol-binding protein. We find no evidence of binding at the putative external binding site in either of these structural analyses. Further, competition between palmitic acid and retinol reveals only palmitate bound to the protein. An explanation is provided for the lack of ligand binding to the orthorhombic crystal form also obtained at pH 7.5. Finally, the possible function of beta-Lg is discussed in the light of its species distribution and similarity to other lipocalins.

Selected figure(s)

Figure 2.
Figure 2. A diagram of the binding site of bovine b-Lg showing the contacts less than 3.9 Å made by retinol to the protein. Notice that there are no obvious contacts of the hydroxyl group to either Lys60 or Lys69, and that the only hydrogen bond involving the ligand appears to be that to Glu62.

Figure 4.
Figure 4. A cladogram derived from the amino acid sequences of b-lactoglobulin, glycodelin and retinol-binding protein. The alignment was carried out by Dr Andrew Coulson and TREEVIEW[58.] was used to produce the diagram. All of the proteins used in the alignment were full-length, mature (no signal sequence is present) b-lactoglobulins with the exception of human glycodelin, labelled Glycodelin, and the 71 amino acid fragment from baboon endometrium, labelled Baboon fra. The sequences were from the SwissProt databank [59.] unless otherwise noted: cow, P02754; cow pseudo-gene; [48.] buffalo, P02755; goat, P02756; goat pseudo-gene, Z47079; sheep, P02757; dolphin, B61590; pig, P04119; dog, P33685; dog III, P33686; cat I, P33687; cat III, P33688; donkey I, P13613; horse I, P02758; donkey II, P19647; horse II, P07380; cat II, P21664; baboon, AF021261; glycodelin, P09466; wallaby, Q29614; kangaroo, P11944; possum, Q29146. For RBP: toad, P06172; chicken, P41263; rat, P27485; human, P02753; horse P19, Q28388.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 318, 1043-1055) copyright 2002.

Figures were selected by the author.