Insights into the Sequence and Structural Diversity of the Nucleotidases Belonging to the Haloacid Dehalogenase Superfamily

The haloacid dehalogenase (HAD) superfamily (HADSF) of enzymes includes nucleotidases, which catalyze the hydrolysis of sugar phosphate bonds in 5'(3') nucleoside monophosphates with specificity for purines and pyrimidines. These enzymes have varied physiological roles and clinical implications. Despite binding of similar substrates and the chemistry of catalysis being the same, the sequences and structures of HADSF nucleotidases show dramatic variability. Despite the availability of structures of many nucleotidases, a comprehensive analysis of similarities and differences is lacking. In this study, we have adopted a bioinformatic approach focusing on HADSF nucleotidases' sequence and structural diversity. The sequence analysis clustered HADSF nucleotidases into functional classes, indicating that sequence-based features are associated with substrate specificities. A common structural feature across the HADSF nucleotidases is the presence of the Rossmannoid core domain with 4 HAD catalytic motifs and a cap domain with varied tertiary structures. Through analysis of these domain structures, we show that the insertion of additional secondary structural elements in the core does not disrupt the architecture of the active site, whereas no such conservation is seen in the cap domain. Finally, a structural phylogeny of the core domains constructed using DALI shows the prokaryotic and eukaryotic nucleotidases grouping into distinct branches. The diversity of the tertiary folds of the cap domain prevented a similar DALI analysis. Interestingly, the cap and core domains of IMP-specific nucleotidase 1, a member of HADSF nucleotidases, have a close structural relationship with certain sugar phosphatases, suggesting a common lineage. This is the first comprehensive study of the structural relationships of HADSF nucleotidases.