Crystal structure of plant defense protein in complex with serine protease

Jaroslav Srp1, 2, Petr Pachl1, 3, Martin Horn1, Michael Mareš1*

1Institute of Organic Chemistry and Biochemistry AS CR, Flemingovo nam. 2, Prague, Czech Republic

2Department of Biochemistry, Faculty of Science, Charles University, Albertov 6, Prague, Czech Republic

3Institute of Molecular Genetics, AS CR, Flemingovo nam. 2, Prague, Czech Republic


Protease inhibitors from the Kunitz family (I3 in MEROPS) of 20-25 kDa are widely distributed in plant kingdom. They share a conserved b-trefoil fold in which a set of variable loops forms reactive centers for the interaction with target proteases. The majority of the Kunitz inhibitors are targeting serine proteases; however, inhibitors of cysteine and aspartic proteases have also been described. PDI (potato cathepsin D inhibitor) from the Kunitz family is a wound inducible plant defense protein against insect herbivores and pathogens. PDI is a unique bifunctional inhibitor of serine proteases as well as aspartic proteases; its binding mode has not been structurally studied so far. Here, we present the crystal structure of the complex of PDI and the serine protease trypsin at 1.95 Å resolution. The binding mode of PDI is compared with that of other Kunitz inhibitors, and structural variability of their reactive centers is discussed.