3ELZ

Crystal structure of Zebrafish Ileal Bile Acid-Bindin Protein complexed with cholic acid (crystal form A).

Summary for 3ELZ

• Entry DOI: 10.2210/pdb3elz/pdb
• Related: 3ELX 3EM0
• Descriptor: ileal Bile Acid-Binding Protein, CHOLIC ACID (3 entities in total)
• Functional Keywords: ileal bile acid-binding protein, zebrafish (danio rerio), cholic acid, lipid-binding, transport, lipid binding protein
• Biological source: Danio rerio (leopard danio,zebra danio,zebra fish)
• Total number of polymer chains: 3
• Total formula weight: 50885.11

Authors

Capaldi, S.,Saccomani, G.,Fessas, D.,Signorelli, M.,Perduca, M.,Monaco, H.L. (deposition date: 2008-09-23, release date: 2009-01-13, Last modification date: 2023-09-06)

Primary citation

Capaldi, S.,Saccomani, G.,Fessas, D.,Signorelli, M.,Perduca, M.,Monaco, H.L.
The X-Ray structure of zebrafish (Danio rerio) ileal bile acid-binding protein reveals the presence of binding sites on the surface of the protein molecule.
J.Mol.Biol., 385:99-116, 2009

PubMed Abstract: The ileal bile acid-binding proteins (I-BABPs), also called ileal lipid-binding proteins or gastrotropins, belong to the family of the fatty acid-binding proteins and play an important role in the solubilization and transport of bile acids in the enterocyte. This article describes the expression, purification, crystallization, and three-dimensional structure determination of zebrafish (Danio rerio) I-BABP both in its apo form and bound to cholic acid. This is the first X-ray structure of an I-BABP. The structure of the apoprotein was determined to a resolution of 1.6 A, and two different monoclinic crystal forms of the holoprotein were solved and refined to 2.2 A resolution. Three protein molecules are present in the asymmetric unit of one of the co-crystal forms and two in the other, and therefore, the results of this study refer to observations made on five different protein molecules in the crystalline state. In every case, two cholate ligands were found bound in approximately the same position in the internal cavity of the protein molecules, but an unexpected result is the presence of clear and unambiguous electron density for several cholate molecules bound on hydrophobic patches on the surface of all the five independent protein molecules examined. Isothermal titration calorimetry was used for the thermodynamic characterization of the binding mechanism and has yielded results that are consistent with the X-ray data. Ligand binding is described in detail, and the conformational changes undergone by the protein molecule in the apo-to-holo transition are examined by superposition of the apo- and holoprotein models. The structure of the holoprotein is also compared with that of the liver BABP from the same species and those of other I-BABPs determined by NMR.

PubMed: 18952094
DOI: 10.1016/j.jmb.2008.10.007

Experimental method

X-RAY DIFFRACTION (2.2 Å)