Transcripts of the myotonic dystrophy protein kinase (DMPK) gene, a member of the Rho kinase family, are subject to cell-type specific alternative splicing. An imbalance in the splice isoform profile of DMPK may play a role in the pathogenesis of DM1, a severe multisystemic disorder. Here, we report how structural subdomains determine biochemical properties and subcellular distribution of DMPK isoforms. A newly developed kinase assay revealed that DMPK is a Lys/Arg-directed kinase. Individual DMPK isoforms displayed comparable transphosphorylation activity and sequence preference for peptide substrates. However, DMPK autophosphorylation and phosphorylation of MYPT1 (as putative in vivo target of DMPK), were dependent on presence of an alternatively spliced VSGGG motif and the nature of the C terminus. In-gel effects of the VSGGG motif on the migration behavior of full-length kinase provide evidence for a model in which this motif mediates 3-D-conformational changes in DMPK isoforms. Finally, different C termini endow DMPK with the ability to bind to either endoplasmic reticulum or mitochondria or to adopt a cytosolic location. Our results suggest that DMPK isoforms have cell-type and location dependent substrate specificities with a role in organellar and cytoarchitectural dynamics.Myotonic dystrophy (DM1) is the most common form of muscular dystrophy in adults (23), caused by amplification of an unstable (CTG) n repeat in the 3Ј untranslated region (3Ј-UTR) of the DM1 protein kinase (DMPK) gene (10,20,29). The severity of the disease is correlated to the length of this repeat expansion, whereas there is an inverse correlation to the age of onset. The favored explanation for the DM1 phenotype is a gain-of-function at the RNA level (reviewed in references 41 and 53), whereby long (CUG) n repeat tracts in DMPK transcripts cause a global perturbation of RNA processing events in the nucleus. Reports of cis-effects on the accumulation of (CUG) n repeat containing DMPK transcripts in the nucleus and trans-effects on alternative splicing of transcripts encoding other muscle or brain proteins support this hypothesis (15,16,30,40,43,45).It is widely accepted, nonetheless, that the highly variable and complex DM1 phenotype is not caused solely by detrimental effects of (CUG) n expansion at the RNA level, but that also direct effects on DMPK gene products and local gene effects are involved in specific disease features. Various studies have shown that expansion of the (CTG) n repeat results in reduced appearance of DMPK in the cytoplasm (53). Studies in knockout mouse and myocyte cell models indicated that lack of DMPK protein may be associated with typical DM1 symptoms like myopathy and heart conduction defects, perhaps via effects on Ca 2ϩ or Na ϩ ion homeostasis (5,6,25,35,42).DMPK is a member of the AGC group of serine/threonine kinases (31) and is most homologous to the p21-activated kinases MRCK (28) and ROCK/rho-kinase/ROK (4). Other mammalian homologues are NDR1 (32), warts/lats (26, 55), and citron kinase (17). DM...