title: Structural basis for the ligand-binding specificity of fatty acid-binding proteins (pFABP4 and pFABP5) in gentoo penguin.
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.
authors.affiliation: Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Republic of Korea.
authors.forename: Chang Woo
authors.initials: CW
authors.lastname: Lee
authors.affiliation: Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea; Department of Pharmacy, Graduate School, Sungkyunkwan University, Suwon 440-746, Republic of Korea.
authors.forename: Jung Eun
authors.initials: JE
authors.lastname: Kim
authors.affiliation: Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea.
authors.forename: Hackwon
authors.initials: H
authors.lastname: Do
authors.affiliation: Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea.
authors.forename: Ryeo-Ok
authors.initials: RO
authors.lastname: Kim
authors.affiliation: Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Republic of Korea.
authors.forename: Sung Gu
authors.initials: SG
authors.lastname: Lee
authors.affiliation: Department of Biochemistry, School of Biotechnology and Graduate School of Biochemistry, Yeungnam University, Gyeongsan, Republic of Korea.
authors.forename: Hyun Ho
authors.initials: HH
authors.lastname: Park
authors.affiliation: Department of Biology Education, Kyungpook National University, Daegu 702-701, Republic of Korea.
authors.forename: Jeong Ho
authors.initials: JH
authors.lastname: Chang
authors.affiliation: Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea.
authors.forename: Joung Han
authors.initials: JH
authors.lastname: Yim
authors.affiliation: Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Republic of Korea.
authors.forename: Hyun
authors.initials: H
authors.lastname: Park
authors.affiliation: Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea. Electronic address: ickim@kopri.re.kr.
authors.forename: Il-Chan
authors.initials: IC
authors.lastname: Kim
authors.affiliation: Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Republic of Korea. Electronic address: junhyucklee@kopri.re.kr.
authors.forename: Jun Hyuck
authors.initials: JH
authors.lastname: Lee
mesh_terms: D000595:Amino Acid Sequence; D000817:Anilino Naphthalenesulfonates; D000818:Animals; D030161:Avian Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D050556:Fatty Acid-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D005456:Fluorescent Dyes; D015870:Gene Expression; D008024:Ligands; D019787:Linoleic Acid / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019308:Palmitic Acid / Q000737:chemistry*; D011485:Protein Binding; D020033:Protein Isoforms / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D046429:Spheniscidae / Q000235:genetics / Q000378:metabolism*
chemical_list: C515594:8-anilino-1-naphthalenesulfonic acid; D000817:Anilino Naphthalenesulfonates; D030161:Avian Proteins; D050556:Fatty Acid-Binding Proteins; D005456:Fluorescent Dyes; D008024:Ligands; D020033:Protein Isoforms; D011994:Recombinant Proteins; D019308:Palmitic Acid; D019787:Linoleic Acid
keywords: Crystal structure; Fatty acid-binding protein; Gentoo penguin (Pygoscelis papua); X-ray crystallography; β-barrel protein