Structural basis for the ligand-binding specificity of fatty acid-binding proteins (pFABP4 and pFABP5) in gentoo penguin

• Published in: Biochemical and biophysical research communications 2015-09, Vol.465 (1), p.12-18
• Main Authors: Lee, Chang Woo, Kim, Jung Eun, Do, Hackwon, Kim, Ryeo-Ok, Lee, Sung Gu, Park, Hyun Ho, Chang, Jeong Ho, Yim, Joung Han, Park, Hyun, Kim, Il-Chan, Lee, Jun Hyuck
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Anilino Naphthalenesulfonates; Animals; Avian Proteins - chemistry; Avian Proteins - genetics; Avian Proteins - metabolism; Cloning, Molecular; Crystal structure; Crystallography, X-Ray; Escherichia coli - genetics; Escherichia coli - metabolism; Fatty acid-binding protein; Fatty Acid-Binding Proteins - chemistry; Fatty Acid-Binding Proteins - genetics; Fatty Acid-Binding Proteins - metabolism; Fluorescent Dyes; Gene Expression; Gentoo penguin (Pygoscelis papua); Ligands; Linoleic Acid - chemistry; Marine; Models, Molecular; Molecular Sequence Data; Palmitic Acid - chemistry; Protein Binding; Protein Isoforms - chemistry; Protein Isoforms - genetics; Protein Isoforms - metabolism; Pygoscelis papua; Recombinant Proteins - chemistry; Recombinant Proteins - genetics; Recombinant Proteins - metabolism; Sequence Alignment; Sequence Homology, Amino Acid; Spheniscidae - genetics; Spheniscidae - metabolism; X-ray crystallography; β-barrel protein
• ISSN: 0006-291X; 1090-2104
• DOI: 10.1016/j.bbrc.2015.07.087

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. •The ligand-binding properties of pFABP4 and pFABP5 were analyzed.•The crystal structure of ligand-unbound pFABP4 was determined.•The crystal structure of linoleate-bound pFABP4 was also determined.•The crystal structure of palmitate-bound pFABP5 was also determined.•The ligand selectivity was explained by structural analysis.