Inositol 1,4,5-trisphosphate 3-kinase, and more generally inositol polyphosphate kinases (Ipk), play important roles in signal transduction in animal cells; however, their functions in plant cells remain to be elucidated. Here, we report the molecular cloning of a cDNA (AtIpk2) from a higher plant, Arabidopsis. Arabidopsis AtIpk2 is a 33-kD protein that exhibits weak homology (25% identical amino acids) with Ipk proteins from animals and yeast and lacks a calmodulin binding site, as revealed by sequence analysis and calmodulin binding assays. However, recombinant AtIpk2 phosphorylates inositol 1,4,5-trisphosphate to inositol 1,4,5,6-tetrakisphosphate and also converts it to inositol 1,3,4,5,6-pentakisphosphate [Ins(1,3,4,5,6)P ₅]. AtIpk2 also phosphorylates inositol 1,3,4,5-tetrakisphosphate to Ins(1,3,4,5,6)P ₅. Thus, the enzyme is a D3/D6 dual-specificity inositol phosphate kinase. AtIpk2 complements a yeast ARG82/IPK2 mutant lacking a functional ArgR-Mcm1 transcription complex. This complex is involved in regulating Arg metabolism-related gene expression and requires inositol polyphosphate kinase activity to function. AtIpk2 was found to be located predominantly in the nucleus of plant cells, as demonstrated by immunolocalization and fusion to green fluorescent protein. RNA gel blot analysis and promoter--glucuronidase reporter gene studies demonstrated AtIpk2 gene expression in various organs tested. These data suggest a role for AtIpk2 as a transcriptional control mediator in plants.