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.