PRTN3 is a serine protease enzyme expressed mainly in neutrophil granulocytes. Its exact role in the function of the neutrophil is unknown but in human neutrophils proteinase 3 contributes to the proteolytic generation of antimicrobial peptides. It is also the epitope of anti-neutrophil cytoplasmic antibodies (ANCAs) of the cANCA (cytoplasmic subtype) class, a type of antibody frequently found in the disease Wegener's granulomatosis.

Proteinase K is commonly used in molecular biology to digest protein and remove contamination from preparations of nucleic acid. Addition of proteinase K to nucleic acid preparations rapidly inactivates nucleases that might otherwise degrade the DNA or RNA during purification.