Crystal structures of a new class of pyrimidine/purine nucleoside phosphorylase (ppnP) revealed a Cupin fold

Abstract

Nucleotides metabolism is a fundamental process in all organisms. Two families of nucleoside phosphorylases (NP) that catalyze the phosphorolytic cleavage of the glycosidic bond in nucleosides have been found, including the trimeric or hexameric NP-I and dimeric NP-II family enzymes. Recently studies revealed another class of NP protein in E. coli named Pyrimidine/purine nucleoside phosphorylase (ppnP), which can catalyze the phosphorolysis of diverse nucleosides and yield D-ribose 1-phosphate and the respective free bases. Here, we solve the crystal structures of ppnP from E. coli and the other three species. Our studies revealed that the structure of ppnP belongs to the Rlmc-like cupin fold and showed as a rigid dimeric conformation. Detail analysis revealed a potential nucleoside binding pocket full of hydrophobic residues. And the residues involved in the dimer and pocket formation are all well conserved in bacteria. Since the cupin fold is a large superfamily in the biosynthesis of natural products, our studies provide the structural basis for understanding and the directed evolution of NP proteins.