Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• APOBEC enzymes catalyze cytosine-to-uracil deamination in single-stranded DNA (ssDNA).
• This process has roles in immunity and is implicated in cancer development, creating characteristic mutation signatures.
• The precise mechanisms of ssDNA recognition and target-sequence selection by APOBEC enzymes are not fully understood.

Purpose of the Study:

• To elucidate the structural mechanisms underlying APOBEC enzyme recognition and binding of ssDNA.
• To understand how APOBEC enzymes achieve dinucleotide specificity in their deamination activity.
• To provide a structural basis for designing inhibitors targeting APOBEC enzymes.

Main Methods:

• X-ray crystallography was used to determine the structures of human APOBEC3A and an APOBEC3B/APOBEC3A chimera bound to ssDNA.
• High-resolution structures were obtained at 3.1-Å and 1.7-Å.
• Analysis of protein-DNA interactions within the crystal structures.

Main Results:

• Crystal structures reveal a U-shaped conformation of ssDNA when bound to APOBEC enzymes.
• The -1 thymine base is flipped out and inserted into a groove, forming hydrogen bonds with the protein.
• The target cytosine is positioned deep within the active site, explaining the 5'-TC sequence preference.
• The structures elucidate conserved and unique properties of APOBEC family members.

Conclusions:

• The study reveals the structural basis for APOBEC3A's ssDNA recognition and 5'-TC sequence specificity.
• These findings explain how APOBEC enzymes generate distinct mutation signatures.
• The structural insights can guide the rational design of inhibitors to target APOBEC activity in viruses and cancer.