Oligomeric Symmetry of Purine Nucleoside Phosphorylases

Abstract

Many enzymes are composed of several identical subunits, which are arranged in a regular fashion and usually comply with some definite symmetry. This symmetry may be approximate or exact and may or may not coincide with the symmetry of crystallographic packing. Purine nucleoside phosphorylases (PNP) are a class of oligomeric enzymes that show an interesting interplay between their internal symmetry and the symmetry of their crystal packings. There are two main classes of this enzyme: trimeric PNPs, or “low-molecular-mass” proteins, which are found mostly in eukaryotic organisms, and hexameric PNPs, or “high-molecular-mass” proteins, which are found mostly in prokaryotic organisms. Interestingly, these two enzyme classes share only 20–30% sequence identity, but the overall fold of the single monomer is similar, yet this monomeric building block results in a different quaternary structure. To investigate this interplay of symmetry in this class of enzymes, a comprehensive database of all PNPs is constructed, containing their local symmetries and interface information.