Planes formed with four intron-positions in tertiary structures of retinol binding protein and calpain domain VI

• We found planes formed with four positions which correspond to intron-positions.
• The plane seems to have relationship with each ligand.
• The planarity is evaluated by average distances from intron-positions to the planes.
• Simulations were performed to get the probabilities of these phenomena.
• The significance of the plane and the evolutionary aspects of RBP are discussed.

Eukaryotic genes have intervening sequences, introns, in their coding regions. Since introns are spliced out from m-RNA before translation, they are considered to have no effect on the protein structure. Here, we report a novel relationship between introns and the tertiary structures of retinol binding protein and calpain domain VI. We identified “intron-positions” as amino acid residues on which or just after which introns are found in their corresponding nucleotide sequences, and then found that four intron-positions form a plane. We also found that the four intron-positions of retinol-binding protein encloses its ligand retinol. The tertiary structure of calpain domain VI changes after Ca2+ binding, and the four intron-positions form a plane that includes its ligand calpastatin. To evaluate the statistical significance of the planarity, we calculated the mean distance of each intron-position from the plane defined by the other three intron-positions, and showed that it is significantly smaller than the one calculated for randomly generated locations based on exon size distribution. On the basis of this finding, we discuss the evolution of retinol binding protein and the origin of introns.