The Structure of Nucleotide Pyrophosphatase/ Phosphodiesterase and Implications for Enzyme Evolution in the Alkaline Phosphatase Superfamily

Abstract

The explosion of recent genomic and structural data is revealing extraordinary evolutionary interrelationships between enzymes with similar active sites that catalyze different reactions. Functional comparisons of these active sites can provide insight into the origins of the enormous catalytic proficiency of enzymes and the evolutionary changes that can lead to different enzyme activities. The alkaline phosphatase (AP) superfamily is an ideal system to make such comparisons given the extensive data available on both non-enzymatic and enzymatic phosphoryl transfer reactions. Some superfamily members, such as AP itself, preferentially hydrolyze phosphate monoesters, whereas others, such as nucleotide pyrophosphatase/ phosphodiesterase (NPP), preferentially hydrolyze phosphate diesters. We have determined the first structure of an NPP family member and show that, as predicted by homology models, the active sites of AP and NPP are nearly identical. Analysis of structural and functional data suggests that a binding site for the diester side chain contributes to preferential diester hydrolysis by NPP. Future work will address the possibility that electrostatic properties of the metal sites also play a role in discrimination between different classes of substrates.