Inositol pyrophosphates: structure, enzymology and function

Abstract

The stereochemistry of the inositol backbone provides a platform on which to generate a vast array of distinct molecular motifs that are used to convey information both in signal transduction and many other critical areas of cell biology. Diphosphoinositol phosphates, or inositol pyrophosphates, are the most recently characterized members of the inositide family. They represent a new frontier with both novel targets within the cell and novel modes of action. This includes the proposed pyrophosphorylation of a unique subset of proteins. We review recent insights into the structures of these molecules and the properties of the enzymes which regulate their concentration. These enzymes also act independently of their catalytic activity via protein-protein interactions. This unique combination of enzymes and products has an important role in diverse cellular processes including vesicle trafficking, endo- and exocytosis, apoptosis, telomere length regulation, chromatin hyperrecombination, the response to osmotic stress, and elements of nucleolar function.

Fig. 1

Structures of inositol pyrophosphates in different organisms. Phosphates are symbolised as a circled P. a Mammalians and yeast and some dictyostelids. The underlying structure is myo-inositol with the one axial hydroxyl, at the 2-position (stereochemical numbering according to NC-IUB). The phosphate at the 2-position is dashed to indicate that both InsP6 and Ins(1,3,4,5,6)P ₅ are common substrates for pyrophosphorylation. Pyrophosphorylations are on the 5- and 1/3-positions. β-Phosphates on the 1/3-position are on white background to indicate that it has not been resolved which enantiomer is present. 5-PP-InsP ₅ is the more abundant PP-InsP ₅. b Inositol pyrophosphates in dictyostelids. Based on myo-inositol. Pyrophosphorylation are on the 5- and 6-position. 6-PP-InsP5 is the most abundant PP-InsP ₅. c Entamoeba histolytica and Phreatamoeba balamuthi. These are based on neo-inositol with two opposite axial hydroxyls, at the 2- and 5-position (numbering analogous to myo-inositol for comparison), on which the pyrophosphorylations occur. Because of the symmetry of neo-inositol only one PP-InsP ₅ exists, 2-PP-InsP ₅

Fig. 2

Metabolic interrelationships of inositol pyrophosphates. Inositol pyrophosphates are involved in complex metabolic interrelationships both with their precursors and each other. Inositol pyrophosphates in parentheses denote structures that are known products of the kinase in vitro but await convincing demonstration in intact, unmodified cells

Fig. 3

IP6Ks showing basic organization of proteins. The figure illustrates the three human IP6Ks (IP6K1, IP6K2, and IP6K3) highlighting their similarities (Blue) and differences (Red) and location of important protein–protein interactions. IP6K1 It is not clear where GRAB binds. However, it is most likely towards the N-terminal as this is a unique region. Rab3A and IP6K1 are both binding partners of GRAB and their hydrophobicity plots bear a passing similarity in this region, too. Proteomic studies have described serine phosphorylation in a WW motif which could indicate interactions with ubiquitin ligase and/or a mitotic protein, and there is a hint of an interaction with the protein RRP42 (see main text). IP6K2 The two distinct regions of IP6K2 serve as unique binding domains for HSP90 and TRAF2. In the case of HSP90 association mutation of either serine 133 or 136 is sufficient to disrupt the association. In contrast, mutations of both serines 347 and 349 are required to prevent TRAF2 association. IP6K3 Apart from its catalytic site there is nothing known about functional motifs in this protein or of any potential interacting partners. Interesting, proteomic studies have revealed phosphorylation of succession of a serine-242, threonine-243 and serine-244. This is in no recognized protein phosphorylation motif, so its function is unclear. However, it is in the region of the catalytic site so may act to regulate enzyme activity

Fig. 4

Cellular functions of inositol pyrophosphates. The stylized figure of the cell illustrates the areas in which inositol pyrophosphates and/or the enzymes that metabolise them play a role. The asterix denotes areas of cell function that may be dependent on the ability of the inositol pyrophosphates to “pyrophosphorylate” proteins. The nucleous is highlighted, not because any specific functions have been elucidated, but because several pyrophosphorylated proteins are thought to be resident there. In addition to the areas highlighted, inositol pyrophosphates regulate phosphate homeostasis and cyclin-complexes in yeast