Autophosphorylation of the activation loop is a common step that converts many protein kinases from an inactive to an active state. Despite the physiological importance of these reactions, the mechanisms that control activation loop autophosphorylation are poorly understood. Smk1 is a meiosis‐specific MAPK in yeast that autophosphorylates its activation loop on tyrosine (Y), thereby upregulating its own catalytic activity. Previously, we identified Isc10 as an inhibitor of Smk1. Here, we show that Isc10 inhibits Smk1 by two mechanisms. First, the C‐terminal segment of Isc10 binds to Smk1 and specifically inhibits the cis‐autophosphorylation of Y209 in its activation‐loop. Second, prior to Smk1 autophosphorylation, the low activity state Smk1 that is bound to Isc10 phosphorylates it on serine 97 (S97). The phosphorylated S97, in turn, becomes trapped in the Smk1 active site. This prevents phosphorylation of downstream targets before activating signals promote Isc10 degradation and the release of active Smk1. Further, Isc10 inhibits autophosphorylation of the mammalian intestinal cell kinase ICK1 (also known as CILK1), suggesting a conserved mechanism of action. Taken together, these findings define a novel class of developmentally‐regulated molecules that inhibit CMGC‐group kinases.
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