X-ray crystallographic structure of a papain-leupeptin complex

Area of Science:

• Structural Biology
• Biochemistry
• Enzymology

Background:

• Papain is a cysteine protease with a well-characterized active site.
• Leupeptin is a known inhibitor of serine and cysteine proteases.
• Understanding enzyme-inhibitor interactions is crucial for drug design.

Purpose of the Study:

• To determine the three-dimensional structure of the papain-leupeptin complex.
• To elucidate the binding mode of leupeptin within the papain active site.
• To provide insights into the mechanism of papain inhibition by leupeptin.

Main Methods:

• X-ray crystallography was employed to determine the complex's structure.
• Data were collected to a resolution of 2.1 Angstroms.
• The R-factor was determined to be 19.8%.

Main Results:

• Leupeptin was observed to interact with the S subsites of the papain active site, not the S' subsites.
• A covalent bond was formed between the inhibitor's carbonyl carbon and the Cys-25 sulfur atom of papain.
• The inhibitor's carbonyl oxygen formed hydrogen bonds with Gln-19 and Cys-25, interacting with the oxyanion hole.

Conclusions:

• The determined structure provides a detailed atomic-level understanding of papain-leupeptin interaction.
• Leupeptin acts as a mechanism-based inhibitor by forming a covalent adduct with papain's active site.
• The findings highlight the importance of the oxyanion hole and specific active site residues in inhibitor binding.