Dormancy Versus Germination: 3D Protein Modeling and Evolutionary Analyses Define the Roles of Genetic Variants in the Barley MKK3 Enzyme

Dormancy is a characteristic of plant seeds that has evolved to avoid exposing the young seedling to adverse weather conditions. The mitogen-activated protein kinase MKK3 from barley is known to mediate the duration of dormancy and subsequent germination of the grain. Here, we used computational and phylogenetic approaches to define the structural model of the monomeric MKK3 domain in complex with the downstream MAPK protein kinase that it phosphorylates. We utilized key genetic variants of the barley MKK3 and generated the structural MKK3/MAPK enzyme-substrate complex, supported by evolutionary analyses, to rationalize the effects of the MKK3 variants occurring at the ATP binding site and in the loops that can be phosphorylated. We propose the likely mechanism of ATP hydrolysis and the effects of common genetic variants on MKK3 activity, thereby influencing the duration of dormancy. The data will facilitate future manipulations of dormancy length in different environments.