5'-Nucleotide phosphodiesterase: features of the substrate binding site as deduced from specificity and kinetics of some novel substrates.

Phosphonate monoesters and phosphate diesters with systematically varied substituents and leaving groups were synthesized and tested as substrates for homogeneous 5'-nucleotide phosphodiesterase from bovine intestine. The enzyme was shown to hydrolyze phosphorothioate and phosphonoamidate compounds but at significantly lower rates than comparable oxy compounds. The effects of bulk and structure of the ester or phosphonate substituents were also investigated. Dibenzyl phosphate, an ester of an aliphatic alcohol, was a poor substrate. The enzyme did not hydrolyze aliphatic monoesters of phosphonates, regardless of bulk. Kinetic parameters of several nitrophenyl phosphonomonoesters and phosphodiesters are presented. The results suggest that synthetic nonnucleotide substrates can bind in two different modes, only one of which is productive. Incidence of nonproductive binding, with consequent kinetic effects, is increased by increasing the symmetry of the substrates.