Crystal structure of inositol polyphosphate 1-phosphatase at 2.3-A resolution

Bovine inositol polyphosphate 1-phosphatase (1-ptase), M(r) = 44,000, is a Mg(2+)-dependent/Li(+)-sensitive enzyme that catalyzes the hydrolysis of the 1-position phosphate from inositol 1,4-bisphosphate and inositol 1,3,4-trisphosphate. We have determined the crystal structure of recombinant bovine 1-ptase in the presence of Mg2+ by multiple isomorphous replacement. The structure is currently refined to an R value of 0.198 for 15,563 reflections within a resolution range of 8.0-2.3 A. 1-Ptase is monomeric in the crystal, consistent with biochemical data, and folds into an alternatively layered alpha/beta/alpha/beta sandwich. The central core of 1-ptase consists of a six-stranded antiparallel beta sheet perpendicular to two parallel three-turn alpha-helices. The beta sheet is flanked by two antiparallel six-turn alpha-helices aligned parallel to the beta sheet, and the central helices are flanked by a five-stranded largely parallel beta sheet. Two neighboring metal binding sites are located in adjacent acidic pockets formed by the intersection of several secondary structure elements including an unusual kink structure formed by the "DPIDST" sequence motif. The fold of 1-ptase is similar to that of two other metal-dependent/Li(+)-sensitive phosphatases, inositol monophosphate phosphatase and fructose 1,6-bisphosphatase despite minimal amino acid identity. Comparison of the active-site pockets of these proteins will likely provide insight into substrate binding and the mechanisms of metal-dependent catalysis and Li+ inhibition.