New structural insights reveal an expanded reaction cycle for inositol pyrophosphate hydrolysis by human DIPP1

Nudix hydrolases attract considerable attention for their wide range of specialized activities in all domains of life. One particular group of Nudix phosphohydrolases (DIPPs), through their metabolism of diphosphoinositol polyphosphates (PP-InsPs), regulates the actions of these polyphosphates upon bioenergetic homeostasis. In the current study, we describe, at an atomic level, hitherto unknown properties of human DIPP1.We provide X-ray analysis of the catalytic core of DIPP1 in crystals complexed with either natural PP-InsPs, alternative PP-InsP stereoisomers, or non-hydrolysable methylene bisphosphonate analogs (PCP-InsPs). The conclusions that we draw from these data are interrogated by studying the impact upon catalytic activity upon mutagenesis of certain key residues. We present a picture of a V-shaped catalytic furrow with overhanging ridges constructed from flexible positively charged side chains; within this cavity, the labile phosphoanhydride bond is appropriately positioned at the catalytic site by an extensive series of interlocking polar contacts which we analogize as suspension cables. We demonstrate functionality for a triglycine peptide within a beta-strand which represents a non-canonical addition to the standard Nudix catalytic core structure. We describe pre-reaction enzyme/substrate states which we posit to reflect a role for electrostatic steering in substrate capture. Finally, through time-resolved analysis, we uncover a chronological sequence of DIPP1/product post-reaction states, one of which may rationalize a role for InsP(6) as an inhibitor of catalytic activity.

Automated summary

Nudix hydrolases, particularly the DIPPs, regulate bioenergetic homeostasis through the metabolism of PP-InsPs. This study reveals the atomic-level properties of human DIPP1, showing a V-shaped catalytic furrow structure with overhanging ridges and demonstrating a non-canonical addition to the standard Nudix catalytic core. Time-resolved analysis uncovers a chronological sequence of DIPP1/product post-reaction states, suggesting a potential role for InsP(6) as an inhibitor of catalytic activity.