The crystal structure of mammalian inositol 1,3,4,5,6-pentakisphosphate 2-kinase reveals a new zinc-binding site and key features for protein function

Inositol 1,3,4,5,6-pentakisphosphate 2-kinases (IP(5) 2-Ks) are part of a family of enzymes in charge of synthesizing inositol hexakisphosphate (IP(6)) in eukaryotic cells. This protein and its product IP(6) present many roles in cells, participating in mRNA export, embryonic development, and apoptosis. We reported previously that the full-length IP(5) 2-K from Arabidopsis thaliana is a zinc metallo-enzyme, including two separated lobes (the N- and C-lobes). We have also shown conformational changes in IP(5) 2-K and have identified the residues involved in substrate recognition and catalysis. However, the specific features of mammalian IP(5) 2-Ks remain unknown. To this end, we report here the first structure for a murine IP(5) 2-K in complex with ATP/IP(5) or IP(6). Our structural findings indicated that the general folding in N- and C-lobes is conserved with A. thaliana IP(5) 2-K. A helical scaffold in the C-lobe constitutes the inositol phosphate-binding site, which, along with the participation of the N-lobe, endows high specificity to this protein. However, we also noted large structural differences between the orthologues from these two eukaryotic kingdoms. These differences include a novel zinc-binding site and regions unique to the mammalian IP(5) 2-K, as an unexpected basic patch on the protein surface. In conclusion, our findings have uncovered distinct features of a mammalian IP(5) 2-K and set the stage for investigations into protein-protein or protein-RNA interactions important for IP(5) 2-K function and activity.