Three-dimensional structure in solution of acyl-coenzyme A binding protein from bovine liver

The three-dimensional structure of acyl-coenzyme A binding protein as encoded by the recombinant gene in Escherichia coli has been determined using nuclear magnetic resonance (n.m.r.) spectroscopy. The structure consists of four alpha-helices A1 (residues 3 to 15), A2 (residues 20 to 36), A3 (residues 51 to 60), and A4 (residues 65 to 85). A1 and A4, and A2 and A3, run in parallel pairs. A2 runs anti-parallel to A1 and A4. The three-dimensional structure of the protein is reminiscent of a shallow bowl with a rim. The "rim" is characterized by many polar and charged groups, whereas the inside and outside surface is predominantly hydrophobic with patches of uncharged polar hydroxyl groups of threonyl, serinyl and tyrosyl residues. The inside bottom contains through two epsilon-amino groups of lysine residues (Lys13 and Lys32) suggesting that the binding site for the nucleotide part of the acyl-coenzyme A part of the ligand molecule is at the inside surface of the bowl. The structure determination was done on the basis of measurements of the intensities of nuclear Overhauser effects (NOEs) and coupling constants that were translated into interatom distance restraints for 833 atom pairs, and 87 dihedral angle restraints, of which 23 were in chiral centers. In all, 42 hydrogen bonds were identified by n.m.r. and provided an additional 84 distance restraints. A total of 20 structures were calculated and the structures can be aligned to a root-mean-square deviation of 0.5 A for the backbone atoms of the residues in the four helices. A region of six residues could not be defined by the restraints obtained by n.m.r. The program Pronto was used for the spectrum analysis in general, and especially for the assignment of the individual NOEs, the integration of the cross peaks, and the measurements of the coupling constants. The programs DIANA and X-PLOR have been used in the structure calculations and evaluations.