Crystallographic and 1H nuclear magnetic resonance studies of 5′-deoxy-5′-adenosineacetic acid; a model nucleotide of adenosine-5′-monophosphate

Abstract

In order to elucidate the substrate specificity of adenosine-5′-monophosphate utilizing enzymes, the spatial conformation of 5′-deoxy-5′-adenosineacetic acid has been studied by X-ray crystallography and ¹H n.m.r. spectroscopy, and the results compared with those for adenosine-5′-monophosphate. In the crystal, the conformation about the glycosyl bond is anti with the torsion angle χ[O(1′)–C(1′)–N(9)–C(8)] equal to 50.7(9)°. The puckering of the ribose ring is C(3′)-exo(₃E). The significant conformational discrepancy between 5′-deoxy-5′-adenosineacetic acid and adenosine-5′-monophosphate was in the orientations of their exocyclic C(4′)–C(5′) bonds: gauche-trans for the former and gauche-gauche for the latter. These conformational characteristics were also observed in ²H₂O solution by ¹H n.m.r. spectroscopy.

The intermolecular hydrogen bonding mode between the carboxyl group and the adenine ring found in the crystal would constitute a good model for the specific interaction between the acidic amino-acid and the nucleic acid base adenine.