Crystallographic refinement and structure of DNase I at 2 A resolution

Area of Science:

• Biochemistry
• Structural Biology
• Enzymology

Background:

• Bovine pancreatic deoxyribonuclease I (DNase I) is an enzyme crucial for DNA degradation.
• Understanding the three-dimensional structure of DNase I is essential for elucidating its catalytic mechanism and biological role.

Purpose of the Study:

• To refine and analyze the high-resolution structure of bovine pancreatic DNase I.
• To identify key structural features contributing to enzyme stability and function.
• To investigate the role of bound calcium ions in DNase I structure.

Main Methods:

• X-ray crystallography at 2 A resolution.
• Restrained parameter, reciprocal least-squares refinement (Hendrickson and Konnert).
• Analysis of bond lengths, angles, non-bonded contacts, and side-chain orientations.

Main Results:

• The refined structure of DNase I was determined with high accuracy (R-factor 0.157).
• Identified extended hydrophobic regions and specific loop structures influencing protein stability and flexibility.
• Revealed the role of two bound calcium ions in stabilizing specific loops and limiting thermal mobility.
• Corrected the amino acid sequence based on structural data, including a tripeptide insertion.

Conclusions:

• The high-resolution structure provides insights into the folding and stability of DNase I.
• The enzyme's structure suggests a possible origin from gene duplication.
• Calcium ions are critical for maintaining the structural integrity of DNase I.
• Structural findings contribute to a deeper understanding of DNase I's enzymatic activity.