We have characterized the positional specificity of the mammalian and yeast VIP/diphosphoinositol pentakisphosphate kinase (PPIP5K) family of inositol phosphate kinases. We deployed a microscale metal dye detection protocol coupled to a high performance liquid chromatography system that was calibrated with synthetic and biologically synthesized standards of inositol pyrophosphates. In addition, we have directly analyzed the structures of biological inositol pyrophosphates using two-dimensional 1 H-1 H and 1 H-31 P nuclear magnetic resonance spectroscopy. Using these tools, we have determined that the mammalian and yeast VIP/ PPIP5K family phosphorylates the 1/3-position of the inositol ring in vitro and in vivo. For example, the VIP/PPIP5K enzymes convert inositol hexakisphosphate to 1/3-diphosphoinositol pentakisphosphate. The latter compound has not previously been identified in any organism. We have also unequivocally determined that 1/3,5-(PP) 2 -IP 4 is the isomeric structure of the bis-diphosphoinositol tetrakisphosphate that is synthesized by yeasts and mammals, through a collaboration between the inositol hexakisphosphate kinase and VIP/PPIP5K enzymes. These data uncover phylogenetic variability within the crown taxa in the structures of inositol pyrophosphates. For example, in the Dictyostelids, the major bis-diphosphoinositol tetrakisphosphate is 5,6-(PP) 2 -IP 4 (Laussmann, T., Eujen, R., Weisshuhn, C. M., Thiel, U., Falck, J. R., and Vogel, G. (1996) Biochem. J. 315, 715-725). Our study brings us closer to the goal of understanding the structure/function relationships that control specificity in the synthesis and biological actions of inositol pyrophosphates.Signal transduction pathways frequently rely on a specific target protein recognizing a precise spatial arrangement of one or more phosphate groups on either another protein or a small metabolite. The six-carbon inositol ring offers what is arguably the most dramatic example of how even subtle modifications to phosphate topology can impart signaling specificity. The combinatorial manner in which phosphate groups can be arranged around the inositol skeleton creates a large family of phosphorylated molecules, many of which have individual, physiological roles (1). The inositol pyrophosphates, such as diphosphoinositol tetrakisphosphate (also known as PP-IP 4 ), PP-IP 5 2 (also known as IP 7 ) and (PP) 2 -IP 4 (also known as IP 8 ) (2, 3), are a specialized subgroup of the inositol-based signaling family that are distinguished by the presence of diphosphate groups. These particular molecules regulate a diverse range of cellular activities, including phosphate sensing, actin cytoskeleton dynamics, apoptosis, vesicle trafficking, transcription, and DNA repair (see Refs. 4 and 5 for reviews). The different isomers of inositol pyrophosphates can be distinguished by biological receptors (6, 7). Thus, there is great interest in understanding the structure/ function relationships of protein interactions with the inositol pyrophosphate ligands.
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