Crystal structure of the amlnoglycosyl antibiotic puromycin dihydrochloride pentahydrate: Models for the terminal 3′-aminoacyladenosine moieties of transfer RNA′s and protein-nucleic acid interactions

Abstract

The structure of puromycin, a broad spectrum antibiotic and a structural analogue of the terminal 3′-aminoacyladenosine moiety of charged transfer tRNA's has been accurately determined using a total of 1968 reflections measured on a diffractometer. The crystals are orthorhombic with space group P2 12 12 1. The unit cell dimensions are: a = 28–642 A,6 = 13–211 A,c = 7–836 A. There are four formula units of puromycin dihydrochloride pentahydrate per unit cell. The structure was solved by a combination of the heavy-atom and tangent refinement methods. Refinement of the structure by the method of full matrix least-squares gave an R value of 0.055, the average estimated standard deviations in bond distances and bond angles are 0.008 Å and 0.4 °, respectively. Puromycin exists as a di-cation, N(1) of the adenine base and the amino group of the amino acid are protonated. Both the adenosyl- and p-methoxyphenylalanyl residues occur in the preferred conformations. The nucleoside is in the anti conformation, X = 19.3 °, with C(3′) endo-C(2′) exo ( 3 T 2) puckering for the ribose, and the gauche-gauche conformation about the C(4′)—C(5′) bond. The amino acid is in the syn conformation about the C(2)—C(3) bond. The peptide group is approximately planar and it, too, exhibits the preferred conformation relative to the ribose. The symmetry related puromycin molecules form a zig-zagging “wall” normal to the ab plane. The water molecules and the chloride ions fill the channels between the walls. There are about twelve hydrogen bonds per molecule of puromycin. The chloride ions show tetrahedral co-ordination, while the water molecules show both three and four co-ordination with variable hydrogen bonding geometries. The adenine bases and the p-methoxyphenyl rings form alternating stacks with interplanar spacing of 3.4 Å. Thus, the structure of puromycin provides a model for intercalation of aromatic rings between nucleic acid bases and a possible mode of interaction of aromatic side chains of proteins with nucleic acid bases. Most significantly the conformation of puromycin provides information on possible conformations for the terminal 3′-aminoacyladenosine moieties of charged tRNA's.