Remote Mutations Induce Functional Changes in Active Site Residues of Human DNA Polymerase β

Area of Science:

• Biochemistry
• Structural Biology
• Molecular Biology

Background:

• Genetic information growth necessitates mutation characterization for disease prediction and therapeutic design.
• Predicting mutation phenotypes is challenging, especially for those lacking obvious structural or chemical implications.

Purpose of the Study:

• To determine the structural basis for the biological phenotype of two cancer variants in DNA polymerase beta (pol β): S229L and G231D.
• To elucidate how these mutations, not readily predictable, influence pol β structure and function.

Main Methods:

• X-ray crystallography was used to determine the structures of the S229L and G231D cancer variants of DNA polymerase beta (pol β).
• Analysis focused on the subtle structural changes and their impact on interactions with neighboring residues and the active site.

Main Results:

• The crystal structures revealed that S229L and G231D mutations subtly alter secondary interactions near the active site.
• These mutations affect the conformational stability of D256, a key residue involved in catalytic metal coordination, via an intervening β-strand (M236).
• The identified mechanism explains the previously unpredictable biological phenotype of these pol β variants.

Conclusions:

• Subtle structural perturbations in DNA polymerase beta (pol β) can significantly impact its function and contribute to disease.
• The findings provide a structural basis for understanding specific cancer variants and may inform targeted therapeutic strategies.
• This work highlights the importance of investigating seemingly minor mutations for a comprehensive understanding of molecular mechanisms in disease.