5BVT

Palmitate-bound pFABP5

Summary for 5BVT

• Entry DOI: 10.2210/pdb5bvt/pdb
• Related: 5BVQ 5BVS
• Descriptor: Epidermal fatty acid-binding protein, PALMITOLEIC ACID (3 entities in total)
• Functional Keywords: fatty acid-binding protein, beta-barrel protein, gentoo penguin (pygoscelis papua), lipid binding protein
• Biological source: Pygoscelis papua
• Total number of polymer chains: 1
• Total formula weight: 15381.90

Authors

Lee, J.H.,Lee, C.W.,Do, H. (deposition date: 2015-06-05, release date: 2015-08-05, Last modification date: 2024-03-20)

Primary citation

Lee, C.W.,Kim, J.E.,Do, H.,Kim, R.O.,Lee, S.G.,Park, H.H.,Chang, J.H.,Yim, J.H.,Park, H.,Kim, I.C.,Lee, J.H.
Structural basis for the ligand-binding specificity of fatty acid-binding proteins (pFABP4 and pFABP5) in gentoo penguin
Biochem.Biophys.Res.Commun., 465:12-18, 2015

PubMed Abstract: Fatty acid-binding proteins (FABPs) are involved in transporting hydrophobic fatty acids between various aqueous compartments of the cell by directly binding ligands inside their β-barrel cavities. Here, we report the crystal structures of ligand-unbound pFABP4, linoleate-bound pFABP4, and palmitate-bound pFABP5, obtained from gentoo penguin (Pygoscelis papua), at a resolution of 2.1 Å, 2.2 Å, and 2.3 Å, respectively. The pFABP4 and pFABP5 proteins have a canonical β-barrel structure with two short α-helices that form a cap region and fatty acid ligand binding sites in the hydrophobic cavity within the β-barrel structure. Linoleate-bound pFABP4 and palmitate-bound pFABP5 possess different ligand-binding modes and a unique ligand-binding pocket due to several sequence dissimilarities (A76/L78, T30/M32, underlining indicates pFABP4 residues) between the two proteins. Structural comparison revealed significantly different conformational changes in the β3-β4 loop region (residues 57-62) as well as the flipped Phe60 residue of pFABP5 than that in pFABP4 (the corresponding residue is Phe58). A ligand-binding study using fluorophore displacement assays shows that pFABP4 has a relatively strong affinity for linoleate as compared to pFABP5. In contrast, pFABP5 exhibits higher affinity for palmitate than that for pFABP4. In conclusion, our high-resolution structures and ligand-binding studies provide useful insights into the ligand-binding preferences of pFABPs based on key protein-ligand interactions.

PubMed: 26206084
DOI: 10.1016/j.bbrc.2015.07.087

Experimental method

X-RAY DIFFRACTION (2.31 Å)