The PA domain is crucial for determining optimum substrate length for soybean protease C1: Structure and kinetics correlate with molecular function

► A homology model of soybean protease C1 is built using tomato subtilase SBT3. ► Molecular interactions correlate with previously published kinetic findings. ► The PA domains interact with the substrates C-terminal to the cleavage site. ► The plant-specific PA domains determine different optimum substrate lengths. ► Optimum substrate length is pertinent to the in vivo function of protease C1.