Structure of papain refined at 1.65 A resolution

Area of Science:

• Biochemistry
• Structural Biology
• Enzymology

Background:

• Papain is a sulfhydryl protease derived from papaya fruit latex.
• It comprises a single polypeptide chain folded into two domains, with an active site located in the groove between them.

Purpose of the Study:

• To refine the crystal structure of papain at 1.65 A resolution.
• To analyze the structural features, including hydrogen bonding and solvent interactions, of the papain molecule.

Main Methods:

• Refinement of the crystal structure using a restrained least-squares procedure.
• Analysis of atomic coordinates, Ramachandran plot angles, and hydrogen bond parameters.
• Identification and characterization of solvent molecules (water and methanol) within the crystal lattice.

Main Results:

• The refined papain structure exhibits an R-factor of 16.1% with atomic coordinate accuracy of 0.1 A.
• Deviations in alpha-helix parameters and diverse hydrogen bonding in beta-sheets were observed.
• Water molecules, particularly internal ones, play a significant role in structural stability, with limited direct protein-protein interactions.

Conclusions:

• The study provides a high-resolution structural model of papain, detailing its secondary structure elements and active site.
• Hydrogen bond formation may not be essential for turn formation in papain.
• The enzyme's structure is stabilized by extensive water-mediated interactions, with the active site being a relatively static region.