Department of Biochemistry and Molecular Pharmacology; Schiffer Lab
Amino Acids, Peptides, and Proteins | Biochemistry | Enzymes and Coenzymes | Genetic Phenomena | Genetics and Genomics | Molecular Biology | Nucleic Acids, Nucleotides, and Nucleosides | Structural Biology
The APOBEC3 (A3) family of human cytidine deaminases is renowned for providing a first line of defense against many exogenous and endogenous retroviruses. However, the ability of these proteins to deaminate deoxycytidines in ssDNA makes A3s a double-edged sword. When overexpressed, A3s can mutate endogenous genomic DNA resulting in a variety of cancers. Although the sequence context for mutating DNA varies among A3s, the mechanism for substrate sequence specificity is not well understood. To characterize substrate specificity of A3A, a systematic approach was used to quantify the affinity for substrate as a function of sequence context, length, secondary structure, and solution pH. We identified the A3A ssDNA binding motif as (T/C)TC(A/G), which correlated with enzymatic activity. We also validated that A3A binds RNA in a sequence specific manner. A3A bound tighter to substrate binding motif within a hairpin loop compared to linear oligonucleotide, suggesting A3A affinity is modulated by substrate structure. Based on these findings and previously published A3A-ssDNA co-crystal structures, we propose a new model with intra-DNA interactions for the molecular mechanism underlying A3A sequence preference. Overall, the sequence and structural preferences identified for A3A leads to a new paradigm for identifying A3A's involvement in mutation of endogenous or exogenous DNA.
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DOI of Published Version
Sci Rep. 2018 May 14;8(1):7511. doi: 10.1038/s41598-018-25881-z. Link to article on publisher's site
Silvas, Tania V.; Hou, Shurong; Myint, Wazo; Nalivaika, Ellen A.; Somasundaran, Mohan; Kelch, Brian A.; Matsuo, Hiroshi; Yilmaz, Nese Kurt; and Schiffer, Celia A., "Substrate sequence selectivity of APOBEC3A implicates intra-DNA interactions" (2018). Open Access Articles. 3475.
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This work is licensed under a Creative Commons Attribution 4.0 License.
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