Specificity Determinants in Phosphoinositide Dephosphorylation: Crystal Structure of an Archetypal Inositol Polyphosphate 5-Phosphatase

Inositol polyphosphate 5-phosphatases are central to intracellular processes ranging from membrane trafficking to Ca2+ signaling, and defects in this activity result in the human disease Lowe syndrome. The 1.8 Å resolution structure of the inositol polyphosphate 5-phosphatase domain of SPsynaptojanin bound to Ca2+ and inositol (1,4)-bisphosphate reveals a fold and an active site His and Asp pair resembling those of several Mg2+-dependent nucleases. Additional loops mediate specific inositol polyphosphate contacts. The 4-phosphate of inositol (1,4)-bisphosphate is misoriented by 4.6 Å compared to the reactive geometry observed in the apurinic/apyrimidinic endonuclease 1, explaining the dephosphorylation site selectivity of the 5-phosphatases. Based on the structure, a series of mutants are described that exhibit altered substrate specificity providing general determinants for substrate recognition.