Structures of human cytosolic and mitochondrial nucleotidases: implications for structure-based design of selective inhibitors

The human 5′(3′)-deoxyribonucleotidases catalyze the dephos­phorylation of deoxyribonucleoside monophosphates to the corresponding deoxyribonucleosides and thus help to maintain the balance between pools of nucleosides and nucleotides. Here, the structures of human cytosolic deoxy­ribonucleotidase (cdN) at atomic resolution (1.08 Å) and mitochondrial deoxyribo­nucleotidase (mdN) at near-atomic resolution (1.4 Å) are reported. The attainment of an atomic resolution structure allowed interatomic distances to be used to assess the probable protonation state of the phosphate anion and the side chains in the enzyme active site. A detailed comparison of the cdN and mdN active sites allowed the design of a cdN-specific inhibitor.